Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

abortCurrentOperation() - Method in class sc.fiji.snt.SNTUI

abortRun - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

abortRun - Variable in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

AbstractAutoTracer - Class in sc.fiji.snt.tracing.auto

Abstract base class for grayscale-based automatic neuron tracers.

AbstractAutoTracer() - Constructor for class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Creates a new AbstractAutoTracer instance.

AbstractConvexHull - Class in sc.fiji.snt.analysis

Parent class for convex hull analysis

AbstractConvexHull(Collection<T>) - Constructor for class sc.fiji.snt.analysis.AbstractConvexHull

AbstractConvexHull(Context, Collection<T>) - Constructor for class sc.fiji.snt.analysis.AbstractConvexHull

AbstractGWDTTracer<T> - Class in sc.fiji.snt.tracing.auto

Abstract base class for GWDT-based tracers: APP2-style neuron tracer using Gray-Weighted Distance Transform and Fast Marching.

AbstractGWDTTracer(RandomAccessibleInterval<T>, double[]) - Constructor for class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Creates a new GWDTTracer.

AbstractGWDTTracer.HierarchySegment - Class in sc.fiji.snt.tracing.auto

Represents a hierarchical segment as defined by APP2.

AbstractGWDTTracer.WaypointBiasSource - Enum Class in sc.fiji.snt.tracing.auto

How the per-waypoint bias amount is derived.

AbstractSearch - Class in sc.fiji.snt.tracing

Abstract class for path-finding over RandomAccessibleIntervals

AbstractSearch(ImagePlus, int, long) - Constructor for class sc.fiji.snt.tracing.AbstractSearch

AbstractSearch(Dataset, int, long) - Constructor for class sc.fiji.snt.tracing.AbstractSearch

AbstractSearch(RandomAccessibleInterval<? extends RealType<?>>, Calibration, int, long) - Constructor for class sc.fiji.snt.tracing.AbstractSearch

AbstractSearch(SNT, ImagePlus) - Constructor for class sc.fiji.snt.tracing.AbstractSearch

AbstractSearch(SNT, RandomAccessibleInterval<? extends RealType<?>>) - Constructor for class sc.fiji.snt.tracing.AbstractSearch

accel(double, int) - Static method in class sc.fiji.snt.viewer.Bvv

Easing functions for keyframe transitions, adapted from BDV movie recorder.

ACCEL_SLOW_END - Static variable in class sc.fiji.snt.viewer.Bvv.Keyframe

ACCEL_SLOW_START - Static variable in class sc.fiji.snt.viewer.Bvv.Keyframe

ACCEL_SOFT_SLOW_END - Static variable in class sc.fiji.snt.viewer.Bvv.Keyframe

ACCEL_SOFT_SLOW_START - Static variable in class sc.fiji.snt.viewer.Bvv.Keyframe

ACCEL_SOFT_SYMMETRIC - Static variable in class sc.fiji.snt.viewer.Bvv.Keyframe

ACCEL_SYMMETRIC - Static variable in class sc.fiji.snt.viewer.Bvv.Keyframe

accelType - Variable in class sc.fiji.snt.viewer.Bvv.Keyframe

Easing type for the transition into this keyframe (0-5).

accentIcon(Color, boolean) - Static method in class sc.fiji.snt.gui.IconFactory

accept(RandomAccessibleInterval<U>) - Method in class sc.fiji.snt.filter.Frangi

accept(RandomAccessibleInterval<U>) - Method in class sc.fiji.snt.filter.SpectralSimilarity

accept(RandomAccessibleInterval<U>) - Method in class sc.fiji.snt.filter.Tubeness

accessToValidImageData() - Method in class sc.fiji.snt.SNT

Checks whether valid image data exists.

accessToValidImagePlus() - Method in class sc.fiji.snt.SNTUI

acronym() - Method in class sc.fiji.snt.annotation.AllenCompartment

acronym() - Method in interface sc.fiji.snt.annotation.BrainAnnotation

Returns the compartment's acronym.

acronym() - Method in class sc.fiji.snt.annotation.DrosophilaCompartment

acronym() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

ACRONYM_ONLY_FORMATTER - Static variable in class sc.fiji.snt.gui.OntologyBrowser

A predefined path formatter that builds a "::"-delimited string using only acronyms.

actionPerformed(ActionEvent) - Method in class sc.fiji.snt.FillManagerUI

actionPerformed(ActionEvent) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

activateFinishedPath - Variable in class sc.fiji.snt.SNT

adapter - Variable in class sc.fiji.snt.viewer.geditor.SNTGraphComponent

adc() - Method in record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.Report

Returns the value of the adc record component.

add(double, double, double) - Method in class sc.fiji.snt.BookmarkManager

BVV mode: adds a marker at the specified world coordinates.

add(double, double, double, Color, float) - Method in class sc.fiji.snt.BookmarkManager

BVV mode: adds a marker at the specified world coordinates with a color and size.

add(int, int, int, double, int, boolean) - Method in class sc.fiji.snt.Fill

Adds a node to the filled structure.

add(int, int, int, int, int) - Method in class sc.fiji.snt.BookmarkManager

Adds a bookmark at the specified coordinates and time/channel positions.

add(int, int, int, ImagePlus) - Method in class sc.fiji.snt.BookmarkManager

add(File[]) - Method in class sc.fiji.snt.viewer.Bvv

Loads reconstruction files and adds them to the viewer with live progress feedback.

add(File[], String) - Method in class sc.fiji.snt.viewer.Viewer3D

Adds a collection of trees or meshes from input files.

add(Object) - Method in class sc.fiji.snt.viewer.Bvv

Script friendly method to add a supported object (Tree, DirectedWeightedGraph) to the viewer overlay.

add(Object) - Method in class sc.fiji.snt.viewer.Viewer2D

Appends a single tree, a single Polygon2D, a collection of Trees, or a collection of Polygon2D to the viewer using default options.

add(Object) - Method in class sc.fiji.snt.viewer.Viewer3D

Script friendly method to add a supported object (Tree, OBJMesh, AbstractDrawable, etc.) to this viewer.

add(String, List<double[]>) - Method in class sc.fiji.snt.BookmarkManager

Adds multiple bookmarks with the specified label and locations.

add(String, List<double[]>, Color) - Method in class sc.fiji.snt.BookmarkManager

Adds multiple bookmarks with the specified label, locations, and color tag.

add(String, List<SNTPoint>, int, int) - Method in class sc.fiji.snt.BookmarkManager

Adds multiple bookmarks with the specified label and locations.

add(List<Tree>, String) - Method in class sc.fiji.snt.viewer.Viewer2D

Adds a list of trees while assigning each tree to a LUT index.

add(Map<Path, Set<Integer>>, String) - Method in class sc.fiji.snt.BookmarkManager

Adds multiple bookmarks from selected path nodes

add(ProfileEntry) - Method in class sc.fiji.snt.analysis.sholl.Profile

add(Path) - Method in class sc.fiji.snt.Path

add(Path) - Method in class sc.fiji.snt.Tree

Adds a new Path to this Tree.

add(Path, int) - Method in class sc.fiji.snt.BookmarkManager

add(SeedPoint) - Method in class sc.fiji.snt.seed.SeedOverlay

Adds a single seed.

add(Tree, String) - Method in class sc.fiji.snt.viewer.Viewer2D

Appends a tree to the viewer.

add(Tree, String, String) - Method in class sc.fiji.snt.viewer.Viewer2D

Appends a tree to the viewer rendered after the specified measurement.

add(Tree, String, String, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D

Appends a tree to the viewer rendered after the specified measurement.

add(Tree, String, ColorTable, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D

Appends a tree to the viewer rendered after the specified measurement.

add(Tree, ColorRGB) - Method in class sc.fiji.snt.viewer.Viewer2D

Appends a tree to the viewer.

addAll(Collection<? extends SeedPoint>) - Method in class sc.fiji.snt.seed.SeedOverlay

Bulk-adds seeds.

addAllenCCFOntology() - Method in class sc.fiji.snt.gui.OntologyBrowser

Convenience method to add the Allen CCF ontology as a tab, including all compartments.

addAllenCCFOntology(boolean) - Method in class sc.fiji.snt.gui.OntologyBrowser

Adds the Allen CCF ontology as a tab.

addAllOntologies() - Method in class sc.fiji.snt.gui.OntologyBrowser

Adds all the default ontologies as tabs.

addAnnotation(SNTPoint, float, Color) - Method in class sc.fiji.snt.viewer.Bvv.AnnotationOverlay

Add a single annotation.

addAnnotations(Collection<SNTPoint>, float, Color) - Method in class sc.fiji.snt.viewer.Bvv.AnnotationOverlay

Add annotations to the current list.

addAsLinesTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class sc.fiji.snt.Path

Deprecated.

addAsLinesTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class sc.fiji.snt.Path

Deprecated.

addBvvToolbarButton(JComponent) - Method in class sc.fiji.snt.BookmarkManager

Adds a component to the BVV toolbar section of this panel.

addCenter() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

addChangeListener(PathChangeListener) - Method in class sc.fiji.snt.Path

addCitationMessage() - Method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

Allows users to visit the manuscript from a dialog prompt

addClearButton(JTextField) - Static method in class sc.fiji.snt.gui.GuiUtils

addClickableURLtoLabel(Component, String, Color) - Static method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

addCloseShortcut(JFrame) - Static method in class sc.fiji.snt.gui.GuiUtils

addColorBarLegend() - Method in class sc.fiji.snt.viewer.Viewer2D

Adds a color bar legend (LUT ramp) to the viewer.

addColorBarLegend(String, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D

addColorBarLegend(String, ColorTable, double, double, int) - Method in class sc.fiji.snt.analysis.SNTChart

Adds a color bar legend (LUT ramp).

addColorBarLegend(ColorTable, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D

Adds a color bar legend (LUT ramp).

addColorBarLegend(ColorTable, double, double) - Method in class sc.fiji.snt.viewer.Viewer3D

Adds a color bar legend (LUT ramp) using default settings.

addColorBarLegend(ColorTable, double, double, boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Adds a color bar legend (LUT ramp) using default settings.

addColorBarLegend(ColorTable, double, double, Font, int, int) - Method in class sc.fiji.snt.viewer.Viewer3D

Adds a color bar legend (LUT ramp).

addColorBarLegend(T) - Method in class sc.fiji.snt.viewer.MultiViewer3D

addColorBarLegend(T) - Method in class sc.fiji.snt.viewer.Viewer2D

Adds a color bar legend (LUT ramp) from a ColorMapper.

addColorBarLegend(T) - Method in class sc.fiji.snt.viewer.Viewer3D

Adds a color bar legend (LUT ramp) from a ColorMapper.

addColorChangedListener(ColorChangedListener) - Method in class sc.fiji.snt.gui.ColorChooserButton

addColumn(String, double[]) - Method in class sc.fiji.snt.analysis.SNTTable

addColumn(String, Collection<Double>) - Method in class sc.fiji.snt.analysis.SNTTable

addDeepOntology(String, Map<String, Object>) - Method in class sc.fiji.snt.gui.OntologyBrowser

Adds a custom ontology tab built from a deeply nested map.

addDiscsTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class sc.fiji.snt.Path

Deprecated.

addDiscsTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class sc.fiji.snt.Path

Deprecated.

addDrosophilaOntology() - Method in class sc.fiji.snt.gui.OntologyBrowser

Adds the Drosophila adult brain ontology (FBbt) as a tab.

addEntry(Path, Color, boolean) - Method in class sc.fiji.snt.MultiPathTracerCanvas

Appends a single entry without repainting

addFill(Fill) - Method in class sc.fiji.snt.PathAndFillManager

addFillerThread(FillerThread) - Method in class sc.fiji.snt.SNT

addGenericColumn(String, Collection<?>) - Method in class sc.fiji.snt.analysis.SNTTable

addGroup(Collection<Tree>, String) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Adds a comparison group to the analysis queue.

addGroup(Collection<Tree>, String, String...) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Adds a comparison group to the analysis queue.

addHelpEntry(PopupMenu, String, Component) - Method in class sc.fiji.snt.gui.PaletteOptions

addHyperlinkMessage(String, Font, Color, String) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

Appends a message to the specified dialog consisting of one or more lines of text, and assigns a functional URL to it.

addLabel(String) - Method in class sc.fiji.snt.viewer.Viewer3D

Adds an annotation label to the scene.

addListener(DocumentListener) - Method in class sc.fiji.snt.gui.FilePicker

addListener(SNTListener) - Method in class sc.fiji.snt.SNT

addListener(CostPalette.Listener) - Method in class sc.fiji.snt.gui.CostPalette

addListener(SigmaPaletteListener) - Method in class sc.fiji.snt.gui.SigmaPalette

addListener(SeedOverlay.SeedOverlayListener) - Method in class sc.fiji.snt.seed.SeedOverlay

Registers a listener (no-op if already registered).

addLutSubmenu(PopupMenu) - Method in class sc.fiji.snt.gui.PaletteOptions

Adds the standard LUT submenu (Default + 7 SNT favourites) to the supplied popup menu.

addMesh(OBJMesh) - Method in class sc.fiji.snt.viewer.Viewer3D

Loads a Wavefront .OBJ file.

addNeighborsToHeap(long[], RandomAccess<T>, PriorityQueue<long[]>, double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Add neighbors to Fast Marching heap.

addNode(DefaultSearchNode, boolean) - Method in class sc.fiji.snt.tracing.SearchThread

addNode(PointInImage) - Method in class sc.fiji.snt.Path

Appends a node to this Path.

addNodes(Collection<SNTPoint>, String, String) - Method in class sc.fiji.snt.viewer.Viewer2D

addNodes(Map<ColorRGB, List<SNTPoint>>) - Method in class sc.fiji.snt.viewer.Viewer2D

addOntology(String, Map<String, List<String>>) - Method in class sc.fiji.snt.gui.OntologyBrowser

Adds a custom ontology tab from a nested map.

addOntology(String, DefaultTreeModel) - Method in class sc.fiji.snt.gui.OntologyBrowser

Adds an ontology tab backed by an existing DefaultTreeModel.

addOptionsMenuItem(JMenuItem) - Method in class sc.fiji.snt.gui.SNTSearchableBar

Adds a menu item to the search bar's options (gear) menu.

addPath(Path) - Method in class sc.fiji.snt.PathAndFillManager

Adds a new path.

addPath(Path, boolean, boolean) - Method in class sc.fiji.snt.PathAndFillManager

addPath(Path, boolean, boolean, boolean) - Method in class sc.fiji.snt.PathAndFillManager

addPath(Path, int, int) - Method in class sc.fiji.snt.PathAndFillManager

addPathAndFillListener(PathAndFillListener) - Method in class sc.fiji.snt.PathAndFillManager

Adds a PathAndFillListener.

addPlaceholder(JTextField, String) - Static method in class sc.fiji.snt.gui.GuiUtils

addPoint(ShollPoint) - Method in class sc.fiji.snt.analysis.sholl.ProfileEntry

addPointDouble(double, double, double) - Method in class sc.fiji.snt.Path

addPoints(double[], double[], double[], String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

addPoints(double[], double[], int) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

addPoints(double[], double[], String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

addPoints(List<double[]>, String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

addPoints(List<Number>, List<Number>, String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

addPoints(List<Number>, List<Number>, List<Number>, String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

addPolygon(Polygon2D, String) - Method in class sc.fiji.snt.viewer.Viewer2D

addPolygon(Polygon2D, String, String) - Method in class sc.fiji.snt.analysis.SNTChart

addPolygon(Polygon2D, ColorRGB, ColorRGB) - Method in class sc.fiji.snt.analysis.SNTChart

addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.tracing.AbstractSearch

Registers a callback to receive progress updates during the search.

addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.tracing.BiSearch

addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.tracing.ManualTracerThread

addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.tracing.SearchThread

addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.tracing.TubularGeodesicsTracer

addSearchArtist(SearchArtist) - Method in class sc.fiji.snt.TracerCanvas

addSelectionListener(Consumer<List<String>>) - Method in class sc.fiji.snt.gui.OntologyBrowser

Registers a listener that is notified whenever the checked selection changes in any tab.

addSeparator(JComponent, String, boolean, GridBagConstraints) - Static method in class sc.fiji.snt.gui.GuiUtils

addSeparator(JComponent, JLabel, boolean, GridBagConstraints) - Static method in class sc.fiji.snt.gui.GuiUtils

addSeparator(JMenu, String) - Static method in class sc.fiji.snt.gui.GuiUtils

addSeparator(JPopupMenu, String) - Static method in class sc.fiji.snt.gui.GuiUtils

addSphere(String, double, double, double, Color, double) - Method in class sc.fiji.snt.SNT

AddTextAnnotationCmd - Class in sc.fiji.snt.gui.cmds

Implements Reconstruction Viewer's 'Add Annotation Label...' commands.

AddTextAnnotationCmd() - Constructor for class sc.fiji.snt.gui.cmds.AddTextAnnotationCmd

Creates a new AddTextAnnotationCmd instance.

addTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class sc.fiji.snt.Path

Deprecated.

This method is deprecated. Use newer 3D visualization methods instead.

addTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class sc.fiji.snt.Path

Deprecated.

This method is deprecated. Use newer 3D visualization methods instead.

addTooltip(JComponent, String) - Static method in class sc.fiji.snt.gui.GuiUtils

addTree(Tree) - Method in class sc.fiji.snt.PathAndFillManager

Adds a Tree.

addTree(Tree) - Method in class sc.fiji.snt.SciViewSNT

Adds a tree to the associated SciView instance.

addTree(Tree) - Method in class sc.fiji.snt.viewer.Bvv

Adds a Tree to the viewer as overlay

addTree(Tree) - Method in class sc.fiji.snt.viewer.Viewer2D

Deprecated.

Use Viewer2D.add(Object) instead

addTree(Tree) - Method in class sc.fiji.snt.viewer.Viewer3D

Adds a tree to this viewer.

addTree(Tree, String) - Method in class sc.fiji.snt.PathAndFillManager

Adds a Tree.

addTrees(Collection<Tree>) - Method in class sc.fiji.snt.PathAndFillManager

Adds a collection of Trees.

addTrees(Collection<Tree>) - Method in class sc.fiji.snt.viewer.Viewer2D

Deprecated.

use Viewer2D.add(Object) instead

addTrees(Collection<Tree>, boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Deprecated.

use Viewer3D.addTrees(Collection, String) instead

addTrees(Collection<Tree>, String) - Method in class sc.fiji.snt.PathAndFillManager

Adds a collection of Trees.

addTrees(Collection<Tree>, String) - Method in class sc.fiji.snt.viewer.Viewer3D

Adds a collection of trees.

addTrees(Collection<Tree>, String, double) - Method in class sc.fiji.snt.viewer.Viewer3D

Adds a collection of trees.

addTrees(Collection<Tree>, String, String...) - Method in class sc.fiji.snt.viewer.Viewer3D

Adds a collection of trees.

addVertex(double, double, double) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

addViewer(Viewer3D) - Static method in class sc.fiji.snt.SNTUtils

addWarningListener(PlausibilityMonitor.WarningListener) - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

addWarnings(List<PlausibilityCheck.Warning>) - Method in class sc.fiji.snt.CurationManager

Appends warnings to the table without replacing existing ones.

ADJUST - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

adjustComponentThroughPrompt(Component) - Method in class sc.fiji.snt.gui.GuiUtils

adjustListPlaceholder() - Method in class sc.fiji.snt.FillManagerUI

affectedPaths() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCheck.Warning

Returns the value of the affectedPaths record component.

afterTracingChoice - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

Algorithm Categories - Search tag in package sc.fiji.snt.tracing.auto

Section

Algorithm Overview - Search tag in package sc.fiji.snt.tracing

Section

aliases() - Method in class sc.fiji.snt.annotation.AllenCompartment

aliases() - Method in interface sc.fiji.snt.annotation.BrainAnnotation

Returns the compartment's alias(es).

aliases() - Method in class sc.fiji.snt.annotation.DrosophilaCompartment

aliases() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

ALIGN_CENTER - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

ALIGN_LEFT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

ALIGN_RIGHT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

ALIVE - Static variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Fast Marching state: voxel distance has been finalized.

AllenCCFRenderer() - Constructor for class sc.fiji.snt.gui.OntologyBrowser.AllenCCFRenderer

AllenCompartment - Class in sc.fiji.snt.annotation

Defines an Allen Reference Atlas (ARA) [Allen Mouse Common Coordinate Framework] annotation.

AllenCompartment(int) - Constructor for class sc.fiji.snt.annotation.AllenCompartment

Instantiates a new ARA annotation from its identifier.

AllenCompartment(UUID) - Constructor for class sc.fiji.snt.annotation.AllenCompartment

Instantiates a new ARA annotation from a UUID (as used by MouseLight's database).

AllenCompartment(JSONObject, UUID) - Constructor for class sc.fiji.snt.annotation.AllenCompartment

AllenUtils - Class in sc.fiji.snt.annotation

Utility methods for accessing/handling AllenCompartments

ALLOWED_MAX_DEGREE - Static variable in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

ALLOWED_MIN_DEGREE - Static variable in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

allPathsShareSameSpatialCalibration() - Method in class sc.fiji.snt.PathAndFillManager

allPointsIterator() - Method in class sc.fiji.snt.PathAndFillManager

AllPointsIterator() - Constructor for class sc.fiji.snt.PathAndFillManager.AllPointsIterator

AlongPathDetector - Class in sc.fiji.snt.analysis.detection

Detects features (boutons, varicosities) along traced paths by analyzing longitudinal radius and intensity profiles.

AlongPathDetector.Config - Class in sc.fiji.snt.analysis.detection

Configuration for along-path detection with builder-like setters.

AlongPathDetectorCmd - Class in sc.fiji.snt.gui.cmds

SciJava command for detecting boutons/varicosities along traced paths using longitudinal radius and intensity profiles.

AlongPathDetectorCmd() - Constructor for class sc.fiji.snt.gui.cmds.AlongPathDetectorCmd

alphaColor(Color, double) - Static method in class sc.fiji.snt.util.SNTColor

Adds an alpha component to an AWT color.

AnalysisUtils - Class in sc.fiji.snt.analysis

Static utilities for sc.fiji.analysis.

analyze(Collection<Path>, double, String) - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Performs growth analysis on a collection of time-matched paths.

analyzeEndpointClusters(Collection<Path>) - Static method in class sc.fiji.snt.util.TreeUtils

Analyzes a collection of paths to determine which endpoint cluster (starts or ends) is more tightly grouped, suggesting the root location.

AnalyzerCmd - Class in sc.fiji.snt.plugin

Deprecated.

replaced by MeasureUI

AnalyzerCmd() - Constructor for class sc.fiji.snt.plugin.AnalyzerCmd

Deprecated.

ANGLE_DOWN - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

ANGLE_RIGHT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

angleDeg() - Method in record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.PolarPeak

Returns the value of the angleDeg record component.

animateLayoutChange - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor

annotate(String) - Method in class sc.fiji.snt.analysis.SNTChart

Adds a subtitle to the chart.

annotate(String, String, String) - Method in class sc.fiji.snt.analysis.SNTChart

Adds a subtitle to the chart.

annotateCategory(String, String) - Method in class sc.fiji.snt.analysis.SNTChart

Annotates the specified category (Category plots only)

annotateCategory(String, String, String) - Method in class sc.fiji.snt.analysis.SNTChart

Annotates the specified category (Category plots only).

annotateLine(Collection<? extends SNTPoint>, String) - Method in class sc.fiji.snt.viewer.Viewer3D

Adds a line annotation to this viewer.

annotateMidPlane(BoundingBox, int, String) - Method in class sc.fiji.snt.viewer.Viewer3D

annotatePlane(SNTPoint, SNTPoint, String) - Method in class sc.fiji.snt.viewer.Viewer3D

annotatePoint(double[], String, String) - Method in class sc.fiji.snt.analysis.SNTChart

Highlights a point in a histogram/XY plot by drawing a labeled arrow at the specified location.

annotatePoint(double, double, String) - Method in class sc.fiji.snt.analysis.SNTChart

Highlights a point in a histogram/XY plot by drawing a labeled arrow at the specified location.

annotatePoint(double, double, String, String) - Method in class sc.fiji.snt.analysis.SNTChart

Highlights a point in a histogram/XY plot by drawing a labeled arrow at the specified location.

annotatePoint(SNTPoint, String) - Method in class sc.fiji.snt.viewer.Viewer3D

Adds a highlighting point annotation to this viewer.

annotatePoint(SNTPoint, String, String, float) - Method in class sc.fiji.snt.viewer.Viewer3D

Adds a highlighting point annotation to this viewer.

annotatePoints(Collection<? extends SNTPoint>, String) - Method in class sc.fiji.snt.viewer.Viewer3D

Adds a scatter (point cloud) annotation to this viewer.

annotateSurface(Collection<? extends SNTPoint>, String) - Method in class sc.fiji.snt.viewer.Viewer3D

annotateSurface(Collection<? extends SNTPoint>, String, boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Computes a convex hull from a collection of points and adds it to the scene as an annotation.

annotateXline(double, String) - Method in class sc.fiji.snt.analysis.SNTChart

Annotates the specified X-value (XY plots and histograms).

annotateXline(double, String, String) - Method in class sc.fiji.snt.analysis.SNTChart

Annotates the specified X-value (XY plots and histograms).

annotateYline(double, String) - Method in class sc.fiji.snt.analysis.SNTChart

Annotates the specified Y-value (XY plots and histograms).

annotateYline(double, String, String) - Method in class sc.fiji.snt.analysis.SNTChart

Annotates the specified Y-value (XY plots and histograms).

Annotation3D - Class in sc.fiji.snt.viewer

An Annotation3D is a triangulated surface or a cloud of points (scatter) rendered in Viewer3D that can be used to highlight nodes in a Tree or locations in a mesh.

Annotation3D(Mesh, String) - Constructor for class sc.fiji.snt.viewer.Annotation3D

Annotation3D(Mesh, ColorRGB, String) - Constructor for class sc.fiji.snt.viewer.Annotation3D

Annotation3D(Polygon2D, ColorRGB, String) - Constructor for class sc.fiji.snt.viewer.Annotation3D

Annotation3D(AbstractConvexHull, ColorRGB, String) - Constructor for class sc.fiji.snt.viewer.Annotation3D

Annotation3D(Viewer3D, Collection<? extends SNTPoint>, int) - Constructor for class sc.fiji.snt.viewer.Annotation3D

Annotation3D(Viewer3D, Collection<Annotation3D>) - Constructor for class sc.fiji.snt.viewer.Annotation3D

Annotation3D(Viewer3D, SNTPoint) - Constructor for class sc.fiji.snt.viewer.Annotation3D

AnnotationDensityCmd - Class in sc.fiji.snt.plugin

Command for obtaining spine/varicosity/synapse/etc. counts from multipoint ROIs or bookmarked locations

AnnotationDensityCmd() - Constructor for class sc.fiji.snt.plugin.AnnotationDensityCmd

AnnotationGraph - Class in sc.fiji.snt.analysis.graph

A specialized graph implementation for brain annotations that extends SNTGraph.

AnnotationGraph() - Constructor for class sc.fiji.snt.analysis.graph.AnnotationGraph

Protected default constructor for internal use.

AnnotationGraph(Collection<Tree>, String, double, int) - Constructor for class sc.fiji.snt.analysis.graph.AnnotationGraph

Constructs an annotation graph from a collection of trees using specified parameters.

AnnotationGraph(Collection<Tree>, Collection<BrainAnnotation>, String) - Constructor for class sc.fiji.snt.analysis.graph.AnnotationGraph

Constructs an annotation graph from trees and annotations using a specified metric.

AnnotationGraph(Collection<Tree>, Collection<BrainAnnotation>, String, double) - Constructor for class sc.fiji.snt.analysis.graph.AnnotationGraph

Constructs an annotation graph from trees and annotations with specified parameters.

AnnotationGraphAdapter - Class in sc.fiji.snt.viewer.geditor

JGraphX adapter for visualizing annotation graphs with brain structures as vertices.

AnnotationGraphAdapter(AnnotationGraph) - Constructor for class sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter

AnnotationGraphAdapter(AnnotationGraph, String) - Constructor for class sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter

AnnotationGraphComponent - Class in sc.fiji.snt.viewer.geditor

JGraphX visualization component for annotation graphs.

AnnotationGraphComponent(AnnotationGraphAdapter, Context) - Constructor for class sc.fiji.snt.viewer.geditor.AnnotationGraphComponent

AnnotationGraphGeneratorCmd - Class in sc.fiji.snt.gui.cmds

SciJava Command for assembling brain annotation connectivity diagrams from tagged neurons, depicting semi-quantitative summaries of targeted brain areas.

AnnotationGraphGeneratorCmd() - Constructor for class sc.fiji.snt.gui.cmds.AnnotationGraphGeneratorCmd

AnnotationGraphRecViewerCmd - Class in sc.fiji.snt.gui.cmds

SciJava Command for displaying annotation graph data in the Reconstruction Viewer with customizable color metrics and mesh opacity.

AnnotationGraphRecViewerCmd() - Constructor for class sc.fiji.snt.gui.cmds.AnnotationGraphRecViewerCmd

AnnotationGraphUtils - Class in sc.fiji.snt.analysis.graph

Utilities for AnnotationGraph handling and manipulation.

AnnotationGraphUtils() - Constructor for class sc.fiji.snt.analysis.graph.AnnotationGraphUtils

AnnotationMapper - Class in sc.fiji.snt.analysis

A specialized ColorMapper for applying color-coded mappings to 3D annotations.

AnnotationMapper(Collection<Annotation3D>) - Constructor for class sc.fiji.snt.analysis.AnnotationMapper

Constructs an AnnotationMapper for the specified collection of 3D annotations.

annotations() - Method in class sc.fiji.snt.viewer.Bvv

AnnotationWeightedEdge - Class in sc.fiji.snt.analysis.graph

Represents a weighted edge between two BrainAnnotation vertices in an annotation graph.

AnnotationWeightedEdge() - Constructor for class sc.fiji.snt.analysis.graph.AnnotationWeightedEdge

ANNULUS - Static variable in interface sc.fiji.snt.analysis.sholl.math.ShollStats

Flag for annulus normalization (Semi-log/Log-log method)

anovaPValue(String) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Computes the one-way ANOVA P-value for all the groups being analyzed.

ANY_HEMISPHERE - Static variable in interface sc.fiji.snt.annotation.BrainAnnotation

Character constant representing any hemisphere (null character)

anyListeners() - Method in class sc.fiji.snt.SNT

anyNodeUnderThreshold(int, int, int, double) - Method in class sc.fiji.snt.tracing.artist.BiSearchArtist

anyNodeUnderThreshold(int, int, int, double) - Method in class sc.fiji.snt.tracing.artist.FillerThreadArtist

anyNodeUnderThreshold(int, int, int, double) - Method in class sc.fiji.snt.tracing.artist.SearchThreadArtist

anySelected() - Method in class sc.fiji.snt.PathAndFillManager

Checks whether at least one Path is currently selected in the UI.

append(Iterator<? extends SNTPoint>) - Method in class sc.fiji.snt.util.BoundingBox

Computes the bounding box of the specified point cloud and appends it to this bounding box, resizing it as needed.

appendLabel(String) - Method in class sc.fiji.snt.gui.CheckboxSpinner

appendSummaryReport(SNTTable) - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Appends summary data of PolarProfileStats.Report to the last row of the specified table Columns written: Angular Distribution Coherence [0,1] Orientation Distribution Coherence [0,1] Preferred Direction in degrees [0,360[ Preferred Orientation in degrees [0,180[ Number of directional peaks Angle, Value of first two directional peaks Number of orientation peaks Angle, Value of first two orientation peaks

appendTimeStamp(String, String) - Method in class sc.fiji.snt.gui.SNTEditorPane

Appends a timestamp to the editor content.

appendToLastRow(String, Object) - Method in class sc.fiji.snt.analysis.SNTTable

Appends a value to the last row in the specified column.

appendToOptionsMenu(Collection<JMenuItem>) - Method in class sc.fiji.snt.gui.SNTSearchableBar

apply() - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

apply(ImgPlus<T>, double) - Static method in class sc.fiji.snt.filter.Tubeness

Apply single-scale tubeness filter to an ImgPlus.

apply(ImgPlus<T>, double[]) - Static method in class sc.fiji.snt.filter.Frangi

Apply multiscale Frangi vesselness filter to an ImgPlus.

apply(ImgPlus<T>, double[]) - Static method in class sc.fiji.snt.filter.Tubeness

Apply multiscale tubeness filter to an ImgPlus.

apply(ImgPlus<T>, double[], double, int) - Static method in class sc.fiji.snt.filter.Frangi

Apply multiscale Frangi vesselness filter to an ImgPlus.

apply(ImgPlus<T>, double[], int) - Static method in class sc.fiji.snt.filter.Tubeness

Apply multiscale tubeness filter to an ImgPlus.

applyAnnularMask(FloatProcessor, double, double) - Static method in class sc.fiji.snt.tracing.CrossSectionUtils

Applies an annular mask to a cross-section FloatProcessor.

applyAnnularMask1D(float[], double, double) - Static method in class sc.fiji.snt.tracing.CrossSectionUtils

Applies an annular mask to a 1D profile.

applyCanvasOffset(double, double, double) - Method in class sc.fiji.snt.Tree

Specifies the offset to be used when rendering this Tree in a TracerCanvas.

applyColorTable(ImagePlus, ColorTable) - Static method in class sc.fiji.snt.util.ImpUtils

applyDefaultCursor(BasicSplitPaneDivider) - Static method in class sc.fiji.snt.gui.GuiUtils.SplitPanes

applyDefaultTags(String...) - Method in class sc.fiji.snt.PathManagerUI

Applies a default (built-in) tag to selected Path(s).

applyEdges(UnaryOperator<E>) - Method in class sc.fiji.snt.analysis.graph.SNTGraph

Apply the given operator over the edge set.

applyFit() - Method in class sc.fiji.snt.PathFitter

Applies the fitted result to the path.

applyLayout(mxIGraphLayout) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

applyLut(String) - Method in class sc.fiji.snt.gui.PaletteOptions

Applies a named ImageJ LUT to the palette image.

applyPlasma(ImagePlus) - Static method in class sc.fiji.snt.util.ColorMaps

Applies the "plasma" colormap to the specified (non-RGB) image

applyPlasma(ImagePlus, int, boolean) - Static method in class sc.fiji.snt.util.ColorMaps

Applies the "plasma" colormap to the specified (non-RGB) image

applyProperties(Tree) - Method in class sc.fiji.snt.Tree

Applies properties from another Tree to this Tree.

applyRoundCorners(JComponent) - Static method in class sc.fiji.snt.gui.GuiUtils

applySelectionFilter(String) - Method in class sc.fiji.snt.PathManagerUI

Selects paths matching a text-based criteria, or a list of SWC type flags

applySelectionFilter(String, Number) - Method in class sc.fiji.snt.PathManagerUI

Selects paths matching a morphometric criteria.

applySelectionFilter(String, Number, Number) - Method in class sc.fiji.snt.PathManagerUI

Selects paths matching a morphometric criteria.

applySettings(MultiSpectralRefiner) - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Applies all settings from another refiner to this one.

applySettings(PathFitter) - Method in class sc.fiji.snt.PathFitter

applyStyle(SNTChart) - Method in class sc.fiji.snt.analysis.SNTChart

applyTag(String) - Method in class sc.fiji.snt.PathManagerUI

Applies a custom tag/ color to selected Path(s).

applyTheme(String) - Method in class sc.fiji.snt.gui.SNTEditorPane

applyTo(PlausibilityMonitor) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCalibrator.CalibrationResult

Applies all calibrated thresholds to the given monitor.

applyTo(AbstractGWDTTracer<T>) - Method in class sc.fiji.snt.tracing.auto.AutoTraceConfig

Applies this configuration to a tracer, setting all derived parameters.

applyTransform(AffineTransform3D) - Method in class sc.fiji.snt.viewer.BvvMultiSource

Applies the given transform as the fixed transform to the leader and all followers.

applyVertices(UnaryOperator<V>) - Method in class sc.fiji.snt.analysis.graph.SNTGraph

Apply the given operator over the vertex set.

applyViridis(ImagePlus) - Static method in class sc.fiji.snt.util.ColorMaps

Applies the "viridis" colormap to the specified (non-RGB) image

applyViridis(ImagePlus, int, boolean) - Static method in class sc.fiji.snt.util.ColorMaps

Applies the "viridis" colormap to the specified (non-RGB) image

applyZCorrection(double) - Method in class sc.fiji.snt.Tree

Applies a Z-shrinkage correction to all nodes in this tree.

approveSelection() - Method in class sc.fiji.snt.gui.FileChooser

appTitle - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor

ARCHIVE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

AREA - Static variable in interface sc.fiji.snt.analysis.sholl.math.ShollStats

Flag for area normalization (Semi-log/Log-log method)

ARRAY - Enum constant in enum class sc.fiji.snt.SNT.SearchImageType

ArraySearchImage<V> - Class in sc.fiji.snt.tracing.image

ArraySearchImage(Class<V>, int, int) - Constructor for class sc.fiji.snt.tracing.image.ArraySearchImage

ArraySearchImageSupplier(Class<V>, int, int) - Constructor for class sc.fiji.snt.tracing.image.SupplierUtil.ArraySearchImageSupplier

ArrayStorageBackend - Class in sc.fiji.snt.tracing.auto.gwdt

In-memory array storage backend using ImgLib2 ArrayImgs.

ArrayStorageBackend(long[]) - Constructor for class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

ARROWS_DLUR - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

ARROWS_LR - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

ARROWS_LR_TO_LINE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

ARROWS_SPLIT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

ARROWS_TO_CIRCLE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

ARROWS_TO_EYE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

asArray() - Method in class sc.fiji.snt.seed.SeedPoint

Returns this seed as a double[]{x, y, z} array.

ascii(ImagePlus, boolean, int, int) - Static method in class sc.fiji.snt.util.ImpUtils

Converts the specified image into ascii art.

askUserConfirmation - Variable in class sc.fiji.snt.SNTUI

asPath(double, double, double, String) - Method in class sc.fiji.snt.tracing.DefaultSearchNode

asPathReversed(double, double, double, String) - Method in class sc.fiji.snt.tracing.DefaultSearchNode

assembleStats(TreeStatistics.StatisticsInstance, String) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

assembleStats(TreeStatistics.StatisticsInstance, String) - Method in class sc.fiji.snt.analysis.PathStatistics

assembleStats(TreeStatistics.StatisticsInstance, String) - Method in class sc.fiji.snt.analysis.TreeStatistics

assessIfBranchesHaveBeenAssigned() - Method in class sc.fiji.snt.analysis.NodeStatistics

assignAnnotationsFromNodeValues(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils

Assigns brain annotations (interpreted as CCF IDs) to node values for all paths in a Tree.

assignBranches(Tree) - Method in class sc.fiji.snt.analysis.NodeStatistics

Associates the nodes being analyzed to the branches of the specified tree

ASSIGNED_VALUE - Static variable in class sc.fiji.snt.analysis.MultiTreeColorMapper

Mapping property: Assigned Tree value

ASSIGNED_VALUE - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics

Flag specifying Tree value statistics

assignEdgeWeightsEuclidean() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

For all edges, sets the Euclidean distance between the source and target vertex as the weight.

assignEditor(GraphEditor) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphComponent

Assigns an editor.

assignHemisphereTags(DirectedWeightedGraph) - Static method in class sc.fiji.snt.annotation.AllenUtils

Assigns hemisphere tags to all nodes in a graph.

assignHemisphereTags(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils

assignIcon(AbstractButton, IconFactory.GLYPH, Color, float) - Static method in class sc.fiji.snt.gui.IconFactory

assignIcon(AbstractButton, IconFactory.GLYPH, Color, Color, float) - Static method in class sc.fiji.snt.gui.IconFactory

assignIcon(AbstractButton, IconFactory.GLYPH, IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory

assignIcon(AbstractButton, IconFactory.GLYPH, IconFactory.GLYPH, float) - Static method in class sc.fiji.snt.gui.IconFactory

assignIcon(JMenuItem, char, boolean, Color) - Static method in class sc.fiji.snt.gui.IconFactory

assignIcon(JMenuItem, IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory

assignImage(ImagePlus) - Method in class sc.fiji.snt.analysis.sholl.Profile

assignImage(ImagePlus) - Method in class sc.fiji.snt.Tree

Assigns the spatial calibration of an image to this Tree.

assignImage(Dataset) - Method in class sc.fiji.snt.Tree

Assigns spatial calibration from a Dataset to this Tree.

assignImage(ImgPlus<?>) - Method in class sc.fiji.snt.Tree

Assigns spatial calibration from an ImgPlus to this Tree.

assignListenerToHelpButton(String, ActionListener) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

Adds a "Help" button and attaches the specified listener to it.

assignPoints(Set<ShollPoint>) - Method in class sc.fiji.snt.analysis.sholl.ProfileEntry

assignPopupToHelpButton(String, JPopupMenu) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

Adds a "Help" button and attaches the specified JPopupMenu to it.

assignPopupToHelpButton(JPopupMenu) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

Attaches the specified JPopupMenu to the GenericDialog "Help" button renamed "More »".

assignProperty(String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

assignRoiZPosition(Roi) - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

Assigns or clears the Z-position on the given ROI based on BinaryTracerCommonCmd.roiPlane and the current mask image.

assignSearchable(JTable, Function<Object, String>, JPopupMenu) - Static method in class sc.fiji.snt.gui.GuiUtils.JTables

assignSpatialSettings(ImagePlus) - Method in class sc.fiji.snt.PathAndFillManager

assignSpatialSettings(Dataset) - Method in class sc.fiji.snt.PathAndFillManager

assignSpatialSettings(ImgPlus<?>) - Method in class sc.fiji.snt.PathAndFillManager

assignToLeftHemisphere(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils

Assigns a tree to the left hemisphere by mirroring it if necessary.

assignToNearestPath(boolean) - Method in class sc.fiji.snt.analysis.detection.AlongPathDetector.Config

Sets AlongPathDetector.Config.assignToNearestPath.

assignToNearestPath(boolean) - Method in class sc.fiji.snt.analysis.detection.LabelProximityDetector.Config

Whether to reassign each detection to the nearest path when multiple paths are close together.

assignToNearestPath(boolean) - Method in class sc.fiji.snt.analysis.detection.PeripathDetector.Config

assignToNearestPaths(List<Detection>, Collection<Path>) - Static method in class sc.fiji.snt.analysis.detection.DetectorUtils

Reassigns each detection to the nearest path (by minimum node distance).

assignToRightHemisphere(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils

Assigns a tree to the right hemisphere by mirroring it if necessary.

assignUniqueColors(Collection<String>) - Method in class sc.fiji.snt.viewer.Viewer3D

assignUniqueColors(Collection<Tree>) - Static method in class sc.fiji.snt.Tree

Deprecated.

use TreeUtils.assignUniqueColors(Collection)

assignUniqueColors(Collection<Tree>) - Static method in class sc.fiji.snt.util.TreeUtils

Assigns distinct colors to a collection of Trees.

assignUniqueColors(Collection<Tree>, String) - Static method in class sc.fiji.snt.Tree

Deprecated.

use TreeUtils.assignUniqueColors(Collection, String)

assignUniqueColors(Collection<Tree>, String) - Static method in class sc.fiji.snt.util.TreeUtils

Assigns distinct colors to a collection of Trees.

assignUniqueColors(Tree) - Static method in class sc.fiji.snt.util.TreeUtils

Assigns distinct colors to paths of a Tree.

assignUniqueColors(Tree, String) - Static method in class sc.fiji.snt.util.TreeUtils

Assigns distinct colors to paths of a Tree.

assignValue(double) - Method in class sc.fiji.snt.Tree

Assigns a numeric property to this Tree.

assignValues() - Method in class sc.fiji.snt.analysis.PathProfiler

Calls PathProfiler.assignValues(Path) on the Paths of the profiled Tree

assignValues(boolean) - Method in class sc.fiji.snt.SNTService

Assigns pixel intensities at each Path node, storing them as Path values.

assignValues(int) - Method in class sc.fiji.snt.analysis.PathProfiler

Retrieves pixel intensities at each node of the Path storing them as Path values

assignValues(Path) - Method in class sc.fiji.snt.analysis.PathProfiler

Retrieves pixel intensities at each node of the Path storing them as Path values

assignValues(Path, int) - Method in class sc.fiji.snt.analysis.PathProfiler

Retrieves pixel intensities at each node of the Path storing them as Path values

ASTAR - Enum constant in enum class sc.fiji.snt.SNT.SearchType

atGoal(int, int, int, boolean) - Method in class sc.fiji.snt.tracing.SearchThread

atGoal(int, int, int, boolean) - Method in class sc.fiji.snt.tracing.TracerThread

ATLAS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

attach(JDialog) - Method in class sc.fiji.snt.gui.SNTCommandFinder

AUTO_INTENSITY_KEY - Static variable in class sc.fiji.snt.gui.cmds.MultiSpectralRefinerCmd

AUTO_THRESHOLD - Static variable in class sc.fiji.snt.analysis.curation.PlausibilityCheck.SignalQuality

Sentinel value indicating the threshold should be inferred from image stats.

AUTO_TUNE_KEY - Static variable in class sc.fiji.snt.gui.cmds.MultiSpectralRefinerCmd

autoCanvasActivation - Variable in class sc.fiji.snt.SNT

autoCT - Variable in class sc.fiji.snt.SNT

AUTOSAVE_KEY - Static variable in class sc.fiji.snt.SNTPrefs

autoSizeColumn(JTable, int, int) - Static method in class sc.fiji.snt.gui.GuiUtils.JTables

Auto-sizes the preferred width of the given column to fit its content, with padding.

autoTrace(List<SNTPoint>, PointInImage) - Method in class sc.fiji.snt.SNT

Automatically traces a path from a list of points and adds it to the active PathAndFillManager instance.

autoTrace(List<SNTPoint>, PointInImage, boolean) - Method in class sc.fiji.snt.SNT

Automatically traces a path from a point A to a point B.

autoTrace(SNTPoint, SNTPoint, PointInImage) - Method in class sc.fiji.snt.SNT

Automatically traces a path from a point A to a point B.

autoTrace(SNTPoint, SNTPoint, PointInImage, boolean) - Method in class sc.fiji.snt.SNT

Automatically traces a path from a point A to a point B.

AutoTraceConfig - Class in sc.fiji.snt.tracing.auto

Derives AbstractGWDTTracer configuration parameters from one or more example paths.

AutoTraceConfigDialog - Class in sc.fiji.snt.gui.cmds

Non-modal dialog displaying AutoTraceConfig results in a JTable with checkboxes, allowing the user to cherry-pick which derived parameters to apply.

AutoTraceConfigDialog(Window, AutoTraceConfig) - Constructor for class sc.fiji.snt.gui.cmds.AutoTraceConfigDialog

Creates the dialog.

AutotraceFromBinarySeedsCmd - Class in sc.fiji.snt.plugin

Batch autotracing wrapper that iterates over the seeds currently held by SNT's SeedOverlay and runs the BinaryTracer (skeleton-based autotracer) once per seed, each seed acting as the root of its own tree.

AutotraceFromBinarySeedsCmd() - Constructor for class sc.fiji.snt.plugin.AutotraceFromBinarySeedsCmd

AutotraceFromBinaryTipsCmd - Class in sc.fiji.snt.plugin

Single-cell skeleton autotracing wrapper that uses the soma ROI on the canvas (or its auto-detection) as the root and the filtered seeds from SNT's SeedOverlay as tip targets.

AutotraceFromBinaryTipsCmd() - Constructor for class sc.fiji.snt.plugin.AutotraceFromBinaryTipsCmd

AutotraceFromSeedsCmd - Class in sc.fiji.snt.plugin

Batch autotracing wrapper that iterates over the seeds currently held by SNT's SeedOverlay and runs the GWDT tracer once per seed (each seed acts as the root of a new Tree).

AutotraceFromSeedsCmd() - Constructor for class sc.fiji.snt.plugin.AutotraceFromSeedsCmd

AutotraceFromTipsCmd - Class in sc.fiji.snt.plugin

Single-cell GWDT autotracing wrapper that uses the soma ROI on the canvas (or the auto-detected soma) as the root and the filtered seeds from SNT's SeedOverlay as tip targets.

AutotraceFromTipsCmd() - Constructor for class sc.fiji.snt.plugin.AutotraceFromTipsCmd

AutotraceFromWaypointsCmd - Class in sc.fiji.snt.plugin

Single-cell GWDT autotracing wrapper that uses the soma ROI on the canvas (or the auto-detected soma) as the root and the filtered seeds from SNT's SeedOverlay as soft path attractors.

AutotraceFromWaypointsCmd() - Constructor for class sc.fiji.snt.plugin.AutotraceFromWaypointsCmd

AutoTracer - Interface in sc.fiji.snt.tracing.auto

Interface for automatic neuron tracers that reconstruct complete neuronal morphologies from images.

AutoTracer.SeedRole - Enum Class in sc.fiji.snt.tracing.auto

Role a SeedPoint plays in a tracing run.

autoTune() - Method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Returns the value of the autoTune record component.

availableLookAndFeels() - Static method in class sc.fiji.snt.gui.GuiUtils

average(Collection<? extends SNTPoint>) - Static method in interface sc.fiji.snt.util.SNTPoint

Computes the average position of a collection of SNTPoints.

average(Collection<Color>) - Static method in class sc.fiji.snt.util.SNTColor

Averages a collection of colors

averageColorAtPositions(ImageStack[], int[][]) - Static method in class sc.fiji.snt.filter.SpectralSimilarity

Computes the average color vector from a set of 3D positions in a multichannel image represented as per-channel ImageStacks.

averageColorAtPositions(RandomAccessibleInterval<T>, int[][]) - Static method in class sc.fiji.snt.filter.SpectralSimilarity

Computes the average color vector from a set of 3D positions in a multichannel image.

averageColorFromPaths(RandomAccessibleInterval<T>, List<Path>, double, double, double) - Static method in class sc.fiji.snt.filter.SpectralSimilarity

Computes the average color vector from path node positions.

averageRate() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhase

Returns the value of the averageRate record component.

AVG_BRANCH_LENGTH - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics

Flag for "Average branch length" analysis.

AVG_CONTRACTION - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics

Flag for "Average contraction" statistics

AVG_FRACTAL_DIMENSION - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics

Flag specifying "Average fractal dimension" statistics

AVG_FRAGMENTATION - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics

Flag for "Average fragmentation" statistics

AVG_PARTITION_ASYMMETRY - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics

Flag specifying "Average partition asymmetry" statistics

AVG_REMOTE_ANGLE - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics

Flag specifying "Average remote bif. angle" statistics

AVG_SPINE_DENSITY - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Deprecated.

Use TreeStatistics.PATH_SPINE_DENSITY instead

AXIAL - Enum constant in enum class sc.fiji.snt.analysis.CircularModels.Domain

axisReport(ImgPlus<?>) - Static method in class sc.fiji.snt.util.ImgUtils

Builds a one-line diagnostic string listing all axes of an ImgPlus with their type, size, and scale.

AXON - Static variable in class sc.fiji.snt.io.MouseLightLoader

The Constant AXON.

AXONAL - Static variable in interface sc.fiji.snt.TreeProperties

B

BACKGROUND_THRESHOLD_KEY - Static variable in class sc.fiji.snt.gui.cmds.MultiSpectralRefinerCmd

backgroundThreshold - Variable in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

backgroundThreshold - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

backgroundThreshold() - Method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Returns the value of the backgroundThreshold record component.

backProject(int, int, int, double, double, double, double, double[], double[]) - Static method in class sc.fiji.snt.tracing.CrossSectionUtils

Back-projects a 2D cross-section grid coordinate to 3D world coordinates.

BackupManagerCmd - Class in sc.fiji.snt.gui.cmds

Manages Tracing Backup files in the workspace.

BackupManagerCmd() - Constructor for class sc.fiji.snt.gui.cmds.BackupManagerCmd

BALANCING_FACTOR - Static variable in class sc.fiji.snt.analysis.RootAngleAnalyzer

balancingFactor() - Method in class sc.fiji.snt.analysis.RootAngleAnalyzer

Returns the balancing factor, computed from RootAngleAnalyzer.centripetalBias().

ballRadiusMultiplier - Static variable in class sc.fiji.snt.SNT

BARCODE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

BETWEENNESS_CENTRALITY - Static variable in class sc.fiji.snt.analysis.graph.GraphColorMapper

Flag for "Betweenness centrality" mapping.

BEZIER_CURVE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

bin() - Method in record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.PolarPeak

Returns the value of the bin record component.

binarize(ImagePlus, double, double) - Static method in class sc.fiji.snt.util.ImpUtils

Binarize an ImagePlus using lower and upper thresholds.

BINARY_MASK - Enum constant in enum class sc.fiji.snt.FillConverter.ResultType

BinaryTracer - Class in sc.fiji.snt.tracing.auto

Class for generation of Trees from a skeletonized image.

BinaryTracer(ImagePlus) - Constructor for class sc.fiji.snt.tracing.auto.BinaryTracer

BinaryTracer(ImagePlus, boolean) - Constructor for class sc.fiji.snt.tracing.auto.BinaryTracer

BinaryTracer(ImagePlus, int) - Constructor for class sc.fiji.snt.tracing.auto.BinaryTracer

BinaryTracer(ImgPlus<T>) - Constructor for class sc.fiji.snt.tracing.auto.BinaryTracer

BinaryTracerCmd - Class in sc.fiji.snt.plugin

Interactive command providing a GUI for BinaryTracer-based autotracing when an image is already loaded in SNT.

BinaryTracerCmd() - Constructor for class sc.fiji.snt.plugin.BinaryTracerCmd

BinaryTracerCommonCmd - Class in sc.fiji.snt.plugin

Abstract base command providing shared parameters and logic for BinaryTracer-based autotracing.

BinaryTracerCommonCmd() - Constructor for class sc.fiji.snt.plugin.BinaryTracerCommonCmd

BinaryTracerFileCmd - Class in sc.fiji.snt.plugin

Non-interactive command for batch BinaryTracer autotracing of all images in a directory.

BinaryTracerFileCmd() - Constructor for class sc.fiji.snt.plugin.BinaryTracerFileCmd

bind(String, Action) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

bind(String, Action, String) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

bind(String, Action, Icon) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

BINOCULARS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

BiSearch - Class in sc.fiji.snt.tracing

A flexible implementation of the bidirectional heuristic search algorithm described in Pijls, W.H.L.M., Post, H., 2009.

BiSearch(RandomAccessibleInterval<? extends RealType<?>>, Calibration, int, int, int, int, int, int, int, long, SNT.SearchImageType, Cost, Heuristic) - Constructor for class sc.fiji.snt.tracing.BiSearch

BiSearch(SNT, int, int, int, int, int, int) - Constructor for class sc.fiji.snt.tracing.BiSearch

BiSearch(SNT, int, int, int, int, int, int, Cost, Heuristic) - Constructor for class sc.fiji.snt.tracing.BiSearch

BiSearch(SNT, RandomAccessibleInterval<? extends RealType<?>>, int, int, int, int, int, int, Cost, Heuristic) - Constructor for class sc.fiji.snt.tracing.BiSearch

BiSearchArtist - Class in sc.fiji.snt.tracing.artist

An artist implementation that visualizes bidirectional search operations.

BiSearchArtist(BiSearch, Color, Color) - Constructor for class sc.fiji.snt.tracing.artist.BiSearchArtist

Constructs a new BiSearchArtist with the specified search and colors.

BiSearchNode - Class in sc.fiji.snt.tracing

A SearchNode which can maintain both a from-start and from-goal search state.

BiSearchNode() - Constructor for class sc.fiji.snt.tracing.BiSearchNode

BiSearchNode(int, int, int) - Constructor for class sc.fiji.snt.tracing.BiSearchNode

BiSearchNode(int, int, int, double, double, double, double, BiSearchNode, BiSearchNode) - Constructor for class sc.fiji.snt.tracing.BiSearchNode

BiSearchNode.State - Enum Class in sc.fiji.snt.tracing

blinkingError(JComponent, String) - Method in class sc.fiji.snt.gui.GuiUtils

BOLD - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

BOOK_READER - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

BOOKMARK - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

BookmarkManager - Class in sc.fiji.snt

Implements the Bookmark Manager pane.

BookmarkManager(SNTUI) - Constructor for class sc.fiji.snt.BookmarkManager

SNT constructor: implements the Bookmark Manager pane embedded in SNT's UI.

BookmarkManager(Bvv) - Constructor for class sc.fiji.snt.BookmarkManager

BVV constructor: implements a standalone marker manager for a BVV viewer.

borderLineCostFactor - Variable in class sc.fiji.snt.gui.cmds.mxOrganicLayoutPrefsCmd

Cost factor applied to energy calculations for node proximity to the notional border of the graph.

bottomBorder(char, boolean) - Static method in class sc.fiji.snt.gui.IconFactory

BOUNDARY_SIZE - Static variable in class sc.fiji.snt.analysis.ConvexHullAnalyzer

boundarySize - Variable in class sc.fiji.snt.analysis.AbstractConvexHull

boundarySize() - Method in class sc.fiji.snt.analysis.AbstractConvexHull

Returns the perimeter (2D) or surface area (3D) of this convex hull.

boundarySize() - Method in class sc.fiji.snt.analysis.ConvexHull2D

boundarySize() - Method in class sc.fiji.snt.analysis.ConvexHull3D

BoundingBox - Class in sc.fiji.snt.util

A BoundingBox contains information (including spatial calibration) of a tracing canvas bounding box, i.e., the minimum bounding cuboid containing all nodes (SNTPoints) of a reconstructed structure.

BoundingBox() - Constructor for class sc.fiji.snt.util.BoundingBox

Constructs an 'empty' BoundingBox using default values, with the box origin defined as a point with Double.NaN coordinates and Double.NaN dimensions

BoundingBox(Collection<? extends SNTPoint>) - Constructor for class sc.fiji.snt.util.BoundingBox

Computes a bounding box from a point cloud.

BOXIVITY - Static variable in class sc.fiji.snt.analysis.ConvexHullAnalyzer

boxPlot(String, DefaultBoxAndWhiskerCategoryDataset) - Static method in class sc.fiji.snt.analysis.AnalysisUtils

BRAIN - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

BRAIN_ROOT_ID - Static variable in class sc.fiji.snt.annotation.AllenUtils

BRAIN_ROOT_ID - Static variable in class sc.fiji.snt.annotation.DrosophilaUtils

Root FBbt numeric ID for "adult brain".

BrainAnnotation - Interface in sc.fiji.snt.annotation

Classes extending this interface implement a neuropil label/annotation aka "compartment".

BrainAnnotationCmd - Class in sc.fiji.snt.plugin

Command to perform distribution analysis of BrainAnnotations on an annotated Tree.

BrainAnnotationCmd() - Constructor for class sc.fiji.snt.plugin.BrainAnnotationCmd

brainAreaAnalysis() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

brainBarycentre() - Static method in class sc.fiji.snt.annotation.ZBAtlasUtils

Returns the spatial centroid of the template brain.

brainBarycentre(String) - Static method in class sc.fiji.snt.annotation.VFBUtils

Returns the spatial centroid of an adult Drosophila template brain.

brainCenter() - Static method in class sc.fiji.snt.annotation.AllenUtils

Returns the spatial centroid of the Allen CCF.

BRANCH_CODE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

BRANCH_CONTRACTION - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Branch contraction"

BRANCH_EXTENSION_ANGLE - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Branch extension angle"

BRANCH_EXTENSION_ANGLE_REL - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Branch extension angle (Rel.)"

BRANCH_EXTENSION_ANGLE_XY - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying Branch extension angle XY

BRANCH_EXTENSION_ANGLE_XZ - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying Branch extension angle XZ

BRANCH_EXTENSION_ANGLE_ZY - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying Branch extension angle ZY

BRANCH_FRACTAL_DIMENSION - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Branch fractal dimension"

BRANCH_LENGTH - Static variable in class sc.fiji.snt.analysis.NodeColorMapper

Flag for "Branch length" analysis.

BRANCH_LENGTH - Static variable in class sc.fiji.snt.analysis.NodeStatistics

Flag for "Branch length" analysis.

BRANCH_LENGTH - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Branch length"

BRANCH_MEAN_RADIUS - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Branch mean radius"

BRANCH_ORDER - Static variable in class sc.fiji.snt.analysis.NodeColorMapper

Flag for "Branch order" statistics.

BRANCH_ORDER - Static variable in class sc.fiji.snt.analysis.NodeStatistics

Flag for "Branch order" statistics.

BRANCH_POINTS - Static variable in class sc.fiji.snt.analysis.graph.AnnotationGraph

BRANCH_SURFACE_AREA - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying Branch surface area statistics.

BRANCH_VOLUME - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying Branch volume statistics.

BranchAngle() - Constructor for class sc.fiji.snt.analysis.curation.PlausibilityCheck.BranchAngle

branchPointIndex - Variable in class sc.fiji.snt.Path

branchTuneMaxAngle - Variable in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

branchTuneMaxAngle - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

BROOM - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

brushBlendRadii(int, int) - Method in class sc.fiji.snt.Path

Smears the center node's radius to flanking nodes using cosine^2-weighted interpolation.

brushMove(int, int, double, double, double) - Method in class sc.fiji.snt.Path

Applies a cosine-squared-weighted displacement to nodes around a center index.

BUG - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

buildDate() - Static method in class sc.fiji.snt.SNTUtils

Retrieves Sholl Analysis implementation date

buildGraph(long[], double[], double) - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

buildGraph(long[], double[], double) - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

buildGraph(long[], double[], double) - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

buildGraph(long[], double[], double) - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Build graph from computed Fast Marching data.

buildMoreButton(Component, String, Consumer<PopupMenu>) - Method in class sc.fiji.snt.gui.PaletteOptions

Builds the standard "More »" button populated with help, LUT submenu, MIP toggle, optional wizard-specific items, snapshot, and dismiss.

buildSpinner() - Method in class sc.fiji.snt.gui.GuiUtils.JTables.VisitingZoom

Builds a JSpinner bound to this state.

BUILT_IN_PRESETS - Static variable in class sc.fiji.snt.analysis.curation.PlausibilityCalibrator

Names of built-in curation presets bundled with SNT (without the .curation extension).

BULB - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

BULLSEYE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

buttonIcon(char, boolean) - Static method in class sc.fiji.snt.gui.IconFactory

buttonIcon(char, boolean, Color) - Static method in class sc.fiji.snt.gui.IconFactory

buttonIcon(IconFactory.GLYPH, float) - Static method in class sc.fiji.snt.gui.IconFactory

buttonIcon(IconFactory.GLYPH, Color, float) - Static method in class sc.fiji.snt.gui.IconFactory

Bvv - Class in sc.fiji.snt.viewer

Support for Big Volume Viewer.

Bvv() - Constructor for class sc.fiji.snt.viewer.Bvv

Constructor for standalone BVV instance.

Bvv(SNT) - Constructor for class sc.fiji.snt.viewer.Bvv

Constructor for assembling a BVV instance tethered to SNT.

BVV_MAX_RENDER_MILLIS - Static variable in class sc.fiji.snt.SNTPrefs

BVV_MAX_STEP_IN_VOXELS - Static variable in class sc.fiji.snt.SNTPrefs

BVV_RENDER_HEIGHT - Static variable in class sc.fiji.snt.SNTPrefs

BVV_RENDER_WIDTH - Static variable in class sc.fiji.snt.SNTPrefs

Bvv.AnnotationOverlay - Class in sc.fiji.snt.viewer

Renders spherical annotations at SNTPoint world coordinates.

Bvv.Keyframe - Class in sc.fiji.snt.viewer

A snapshot of the BVV viewer state at a particular moment, used as a keyframe for movie recording.

Bvv.PathRenderingOptions - Class in sc.fiji.snt.viewer

Configuration options for path rendering.

BvvCmd - Class in sc.fiji.snt.gui.cmds

Convenience command for starting a standalone Bvv instance.

BvvCmd() - Constructor for class sc.fiji.snt.gui.cmds.BvvCmd

BvvMultiSource - Class in sc.fiji.snt.viewer

A group of BvvSource objects that are treated as a logical unit: display properties (color, range, active state) and manual transforms applied to the leader source are propagated to all follower sources.

BvvMultiSource(BvvStackSource<?>) - Constructor for class sc.fiji.snt.viewer.BvvMultiSource

Convenience constructor for a single source (no followers).

BvvMultiSource(BvvStackSource<?>, List<BvvStackSource<?>>) - Constructor for class sc.fiji.snt.viewer.BvvMultiSource

Creates a group with a designated leader and zero or more followers.

BvvRenderingOptionsCmd - Class in sc.fiji.snt.gui.cmds

Command providing a GUI for configuring Bvv.PathRenderingOptions.

BvvRenderingOptionsCmd() - Constructor for class sc.fiji.snt.gui.cmds.BvvRenderingOptionsCmd

C

CABLE_LENGTH - Static variable in class sc.fiji.snt.analysis.MultiTreeColorMapper

Mapping property: Cable length

cal - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

CALCULATOR - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

calibrate() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCalibrator

Runs the calibration against all reference trees and returns a PlausibilityCalibrator.CalibrationResult containing the inferred thresholds.

CalibratedSource(RandomAccessibleInterval<T>, T, AffineTransform3D, String, double[], String) - Constructor for class sc.fiji.snt.io.SpimDataUtils.CalibratedSource

Convenience constructor for sources without a time axis (timeDim = -1).

CalibratedSource(RandomAccessibleInterval<T>, T, AffineTransform3D, String, double[], String, int) - Constructor for class sc.fiji.snt.io.SpimDataUtils.CalibratedSource

Full constructor.

calibrateFromTrees(List<Tree>) - Method in class sc.fiji.snt.CurationManager

Calibrates thresholds from the given in-memory trees, enables live monitoring, runs a full scan, and switches SNTUI to the Assistant tab.

CalibrationResult() - Constructor for class sc.fiji.snt.analysis.curation.PlausibilityCalibrator.CalibrationResult

calibrationToAxes(Calibration, int) - Static method in class sc.fiji.snt.util.ImpUtils

Creates ImgPlus axes from IJ1 Calibration

call() - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Runs the multispectral refinement on this path.

call() - Method in class sc.fiji.snt.analysis.ProfileProcessor

Process and return the profile values.

call() - Method in class sc.fiji.snt.PathFitter

Takes the signal from the image specified in the constructor to fit cross-section circles around the nodes of input path.

CAMERA - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

cancel() - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

cancel() - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

cancel() - Method in class sc.fiji.snt.plugin.PathMatcherCmd

cancel() - Method in class sc.fiji.snt.plugin.ShollAnalysisTreeCmd

cancel(String) - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

cancel(String) - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

cancel(String) - Method in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

cancelAndFreezeUI(String) - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCommonCmd

cancelFit(boolean) - Method in class sc.fiji.snt.PathManagerUI

CANCELLED - Static variable in class sc.fiji.snt.tracing.SearchThread

cancelPath() - Method in class sc.fiji.snt.SNT

Cancels the temporary path.

cancelSearch(boolean) - Method in class sc.fiji.snt.SNT

cancelSelection() - Method in class sc.fiji.snt.gui.FileChooser

cancelTemporary() - Method in class sc.fiji.snt.SNT

canFormContinuousChain(Collection<Path>, double) - Static method in class sc.fiji.snt.util.TreeUtils

Checks if a collection of paths can form a spatially continuous chain within a given tolerance.

canvasOffset - Variable in class sc.fiji.snt.Path

canvasResized() - Method in class sc.fiji.snt.PathAndFillManager

Deprecated.

captureKeyframe() - Method in class sc.fiji.snt.viewer.Bvv

Captures the current viewer state as a Bvv.Keyframe.

captureView(String, boolean) - Method in class sc.fiji.snt.SNT

Retrieves a WYSIWYG 'snapshot' of a tracing canvas.

captureView(String, ColorRGB) - Method in class sc.fiji.snt.SNT

Retrieves a WYSIWYG 'snapshot' of a tracing canvas without voxel data.

CARET_DOWN - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

CARET_UP - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

CARET_UP_DOWN - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

CASE_BUTTON - Static variable in class sc.fiji.snt.gui.SearchField

caseButton() - Method in class sc.fiji.snt.gui.SearchField

cellLabelChanged(Object, Object, boolean) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter

center - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

center - Variable in class sc.fiji.snt.util.CircleCursor3D

center() - Method in class sc.fiji.snt.analysis.sholl.Profile

center() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Returns the value of the center record component.

centeredMsg(String, String) - Method in class sc.fiji.snt.gui.GuiUtils

centeredMsg(String, String, String) - Method in class sc.fiji.snt.gui.GuiUtils

centerGraph() - Method in class sc.fiji.snt.viewer.geditor.SNTGraphComponent

centerOneTouchButtons(JSplitPane, BasicSplitPaneDivider) - Static method in class sc.fiji.snt.gui.GuiUtils.SplitPanes

centerOnParent(Component, Window) - Static method in class sc.fiji.snt.gui.GuiUtils

centerOnParent(Rectangle, Window) - Static method in class sc.fiji.snt.gui.GuiUtils

centerPoint - Variable in class sc.fiji.snt.util.CircleCursor3D

centerWindow(Window, Window...) - Static method in class sc.fiji.snt.gui.GuiUtils

CENTRIPETAL_BIAS - Static variable in class sc.fiji.snt.analysis.RootAngleAnalyzer

centripetalBias() - Method in class sc.fiji.snt.analysis.RootAngleAnalyzer

Returns the strength of the centripetal bias, also known as κ.

centroid() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Returns the value of the centroid record component.

cGraph - Variable in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter

changeState(int) - Method in class sc.fiji.snt.SNTUI

Changes this UI to a new state.

changeState(FillManagerUI.State) - Method in class sc.fiji.snt.FillManagerUI

Changes this UI to a new state.

changeTracker - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor

changeUIState(int) - Method in class sc.fiji.snt.SNT

channel - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

channel - Variable in class sc.fiji.snt.seed.SeedPoint

1-based channel index, or SeedPoint.CT_UNSET.

channel - Variable in class sc.fiji.snt.SNT

channelIndex() - Method in record class sc.fiji.snt.util.ImgUtils.SliceResult

Returns the value of the channelIndex record component.

channelSum(double[]) - Static method in class sc.fiji.snt.filter.SpectralSimilarity

Sums all elements of a vector.

CHART - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

CHART_AREA - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

CHART_LINE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

CHART_MAGNIFIED - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

CHART_PIE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

chebyshevDxTo(PointInImage) - Method in class sc.fiji.snt.util.PointInImage

chebyshevXYdxTo(PointInImage) - Method in class sc.fiji.snt.util.PointInImage

chebyshevZdxTo(PointInImage) - Method in class sc.fiji.snt.util.PointInImage

check(Path, Path, int) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.BranchAngle

check(Path, Path, int) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.ConstantRadii

check(Path, Path, int) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.DirectionContinuity

check(Path, Path, int) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.LiveCheck

Evaluates the plausibility of a child path forking from a parent.

check(Path, Path, int) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.RadiusContinuity

check(Path, Path, int) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.SomaDistance

For this check, parent is ignored: it evaluates whether the child's first node is within range of any soma path.

check(Path, Path, int) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.TerminalBranchLength

check(Path, Path, int) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.TortuosityConsistency

CHECK_DOUBLE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

checkboxMenuItem(String, boolean, ActionListener, KeyStroke) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

Creates a checkbox menu item with a right-aligned shortcut hint and no global accelerator binding.

CheckboxSpinner - Class in sc.fiji.snt.gui

A custom GUI component combining a checkbox and spinner control in a single panel.

CheckboxSpinner(JCheckBox, JSpinner) - Constructor for class sc.fiji.snt.gui.CheckboxSpinner

checkboxWithoutAccelerator(String, boolean) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

checkDistance(PointInImage, List<PointInImage>) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.SomaDistance

Evaluates distance from a point to the nearest soma location.

checkName() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCalibrator.CheckSummary

Returns the value of the checkName record component.

checkName() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCheck.Warning

Returns the value of the checkName record component.

checkStatus() - Method in class sc.fiji.snt.tracing.BiSearch

checkStatus() - Method in class sc.fiji.snt.tracing.SearchThread

CheckSummary(String, String, double, int, double, double, double) - Constructor for record class sc.fiji.snt.analysis.curation.PlausibilityCalibrator.CheckSummary

Creates an instance of a CheckSummary record class.

checkUnsetFields() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

checkUnsetFields(boolean) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

CHILD - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

children - Variable in class sc.fiji.snt.Path

CHILDREN - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

childrenAsString() - Method in class sc.fiji.snt.Path

ChooseDataset - Class in sc.fiji.snt.plugin

Implements "Choose New Dataset" command for SNTUI.

ChooseDataset() - Constructor for class sc.fiji.snt.plugin.ChooseDataset

ChooseDatasetCmd - Class in sc.fiji.snt.gui.cmds

Implements the 'Choose Tracing Image (From Open Image)...' command.

ChooseDatasetCmd() - Constructor for class sc.fiji.snt.gui.cmds.ChooseDatasetCmd

chosenImp - Variable in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

chosenMaskImp - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

circle(double, double, double) - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutGrouped

circle(Object[], double, double, double) - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutScaled

circle(Object[], double, double, double) - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutSorted

CIRCLE - Enum constant in enum class sc.fiji.snt.analysis.ProfileProcessor.Shape

CIRCLE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

CIRCLE2D - Static variable in class sc.fiji.snt.analysis.PathProfiler

CIRCLE3D - Static variable in class sc.fiji.snt.analysis.PathProfiler

CircleCursor3D<T> - Class in sc.fiji.snt.util

Iterate the pixels of an oriented circle in 3-space using Bresenham's algorithm, where the circle is constructed from the unit normal to the circle plane, the center point, and radius.

CircleCursor3D(RandomAccessible<T>, Localizable, long, double[]) - Constructor for class sc.fiji.snt.util.CircleCursor3D

Iterates over a Bresenham circle in the target RandomAccessible.

CircleCursor3D(RandomAccessible<T>, Localizable, long, double[], double[]) - Constructor for class sc.fiji.snt.util.CircleCursor3D

Iterates over a Bresenham circle in the target RandomAccessible.

CircularModels - Class in sc.fiji.snt.analysis

Shared utilities for circular modeling, including von Mises fits.

CircularModels.Domain - Enum Class in sc.fiji.snt.analysis

Domain of the angle data.

CircularModels.VonMisesFit - Record Class in sc.fiji.snt.analysis

Immutable summary of a von Mises fit on circular (directional) or axial (orientation) data.

citationMsg() - Static method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

citationURL() - Static method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

classify(DirectedWeightedGraph, boolean) - Static method in class sc.fiji.snt.analysis.StrahlerAnalyzer

clear() - Method in class sc.fiji.snt.analysis.SNTTable

clear() - Method in class sc.fiji.snt.PathAndFillManager

Deletes all paths and fills.

clear() - Method in class sc.fiji.snt.seed.SeedOverlay

Removes all seeds.

clear() - Method in class sc.fiji.snt.viewer.Bvv.AnnotationOverlay

Remove all annotations.

clearAll() - Method in class sc.fiji.snt.gui.cmds.PrefsCmd

Clears all of SNT preferences.

clearAll() - Static method in class sc.fiji.snt.SNTPrefs

clearAllTrees() - Method in class sc.fiji.snt.viewer.Bvv

Clears all rendered trees from the overlay.

clearEntries() - Method in class sc.fiji.snt.MultiPathTracerCanvas

Clears all entries

clearForkContext() - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

Clears the cached fork context.

clearReview(Path) - Static method in class sc.fiji.snt.analysis.curation.CurationTags

Removes every cur:* suffix from path's name.

clearSelection() - Method in class sc.fiji.snt.BookmarkManager

Clears the selection of bookmarks in the table.

clearSelection() - Method in class sc.fiji.snt.gui.OntologyBrowser

Clears all checked selections across all tabs.

clearSelection() - Method in class sc.fiji.snt.PathManagerUI

Clears the current path selection.

clearSelection() - Method in class sc.fiji.snt.seed.SeedOverlay

Clears the selection.

clearSlabZBounds() - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Clears slab Z bounds (reverts to no slab culling).

clearStatus() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

clickAtMaxPoint(int, int, int, boolean) - Method in class sc.fiji.snt.SNT

clickForTrace(double, double, double, boolean) - Method in class sc.fiji.snt.SNT

clickForTrace(double, double, int, boolean) - Method in class sc.fiji.snt.SNT

clickForTrace(Point3d, boolean) - Method in class sc.fiji.snt.SNT

CLIPBOARD - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

CLOCK_ROTATE_LEFT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

clone() - Method in class sc.fiji.snt.analysis.graph.AnnotationWeightedEdge

clone() - Method in class sc.fiji.snt.analysis.graph.SWCWeightedEdge

clone() - Method in class sc.fiji.snt.Path

Creates a deep copy of this Path.

clone() - Method in class sc.fiji.snt.Path.PathNode

Creates a deep copy of this PathNode.

clone() - Method in class sc.fiji.snt.Tree

Creates a deep copy of this Tree.

clone() - Method in class sc.fiji.snt.util.BoundingBox

Creates a copy of this BoundingBox.

clone() - Method in class sc.fiji.snt.util.PointInImage

Creates a copy of this PointInImage.

clone(boolean) - Method in class sc.fiji.snt.Path

Creates a copy of this Path with optional inclusion of immediate children.

CLONE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

closeAll() - Static method in class sc.fiji.snt.analysis.SNTChart

Closes all open charts

closeAndResetAllPanes() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

closeAndResetAllPanes() - Method in class sc.fiji.snt.SNT

CLOSED - Enum constant in enum class sc.fiji.snt.tracing.BiSearchNode.State

CLOSED_FROM_GOAL - Static variable in class sc.fiji.snt.tracing.SearchThread

closed_from_goal_count - Variable in class sc.fiji.snt.tracing.BiSearch

closed_from_goal_count - Variable in class sc.fiji.snt.tracing.SearchThread

CLOSED_FROM_START - Static variable in class sc.fiji.snt.tracing.SearchThread

closed_from_start_count - Variable in class sc.fiji.snt.tracing.BiSearch

closed_from_start_count - Variable in class sc.fiji.snt.tracing.SearchThread

closeSplashScreen() - Static method in class sc.fiji.snt.gui.GuiUtils

closestIntersection - Variable in class sc.fiji.snt.NearPoint

CLOUD - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

clusterCentroid() - Method in record class sc.fiji.snt.util.TreeUtils.EndpointClusterAnalysis

Returns the value of the clusterCentroid record component.

cmdService - Variable in class sc.fiji.snt.viewer.geditor.SNTGraphComponent

cnnType - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

CODE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

CODE2 - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

COG - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

COGS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

COL_CONFIDENCE - Static variable in class sc.fiji.snt.seed.SeedTableModel

COL_RADIUS - Static variable in class sc.fiji.snt.seed.SeedTableModel

COL_SOURCE - Static variable in class sc.fiji.snt.seed.SeedTableModel

COL_STATUS - Static variable in class sc.fiji.snt.seed.SeedTableModel

Coverage status (derived).

COL_TYPE - Static variable in class sc.fiji.snt.seed.SeedTableModel

COL_X - Static variable in class sc.fiji.snt.seed.SeedTableModel

COL_Y - Static variable in class sc.fiji.snt.seed.SeedTableModel

COL_Z - Static variable in class sc.fiji.snt.seed.SeedTableModel

collapseAllNodes(JTree) - Static method in class sc.fiji.snt.gui.GuiUtils.JTrees

collapseNodesOfSameLevel(JTree, TreePath) - Static method in class sc.fiji.snt.gui.GuiUtils.JTrees

collapseSomaNodes(DirectedWeightedGraph, double, double, double) - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Core method to collapse soma nodes to a centroid.

collapseSomaToRoiCentroid(DirectedWeightedGraph) - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Collapses all soma nodes to the geometric ROI centroid.

collapseSomaToWeightedCentroid(DirectedWeightedGraph) - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Collapses all soma nodes to their weighted centroid.

CollapsiblePanel - Class in sc.fiji.snt.gui

A user-triggered collapsible panel.

CollapsiblePanel(String, Component) - Constructor for class sc.fiji.snt.gui.CollapsiblePanel

Constructs a new CollapsiblePanel with the specified header and contents.

CollapsiblePanel(String, Component, boolean) - Constructor for class sc.fiji.snt.gui.CollapsiblePanel

Default constructor.

collectChildren(Path, Collection<Path>) - Static method in class sc.fiji.snt.util.TreeUtils

Collects direct children of a path into the provided collection.

collectDescendants(Path, Collection<Path>) - Static method in class sc.fiji.snt.util.TreeUtils

Collects all descendants (children, grandchildren, etc.) of a path into the provided collection.

collectionAsReader(Collection<SWCPoint>) - Static method in class sc.fiji.snt.util.SWCPoint

Converts a collection of SWC points into a Reader.

collectPlots() - Static method in class sc.fiji.snt.gui.cmds.SaveMeasurementsCmd

color() - Method in class sc.fiji.snt.annotation.AllenCompartment

color() - Method in interface sc.fiji.snt.annotation.BrainAnnotation

Returns the display color of this compartment (if known).

color() - Method in class sc.fiji.snt.annotation.DrosophilaCompartment

color() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

color() - Method in record class sc.fiji.snt.MultiPathTracerCanvas.Entry

Returns the value of the color record component.

color() - Method in class sc.fiji.snt.util.SNTColor

Retrieves the AWT color

COLOR - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

COLOR_SOMA_MESH - Static variable in class sc.fiji.snt.gui.cmds.AnnotationGraphRecViewerCmd

COLOR_UNIQUE - Static variable in class sc.fiji.snt.gui.cmds.AnnotationGraphRecViewerCmd

COLOR_WEIGHT_KEY - Static variable in class sc.fiji.snt.gui.cmds.MultiSpectralRefinerCmd

COLOR2 - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

colorChanged(Color) - Method in interface sc.fiji.snt.gui.ColorChangedListener

Called when a color has been changed.

ColorChangedListener - Interface in sc.fiji.snt.gui

Interface for monitoring changes in ColorChooserButton.

colorChooser(Color) - Static method in class sc.fiji.snt.gui.GuiUtils

ColorChooserButton - Class in sc.fiji.snt.gui

Creates a JButton holding a color chooser.

ColorChooserButton(Color, String) - Constructor for class sc.fiji.snt.gui.ColorChooserButton

ColorChooserButton(Color, String, double, int) - Constructor for class sc.fiji.snt.gui.ColorChooserButton

colorCode(String, String) - Method in class sc.fiji.snt.viewer.Annotation3D

colorCode(String, String, ColorTable) - Method in class sc.fiji.snt.viewer.Viewer3D

Runs TreeColorMapper on the specified Tree.

colorCode(Collection<String>, String, ColorTable) - Method in class sc.fiji.snt.viewer.Viewer3D

Runs MultiTreeColorMapper on the specified collection of Trees.

colorForSeed(ColorTable, SeedOverlay.ColorMode, SeedPoint, double, double, double, Map<SeedPoint, Integer>, Map<String, Integer>) - Static method in class sc.fiji.snt.SeedOverlayRenderer

Dispatches to the per-mode color computation.

colorImage - Variable in class sc.fiji.snt.SNT

ColorMapper - Class in sc.fiji.snt.analysis

Parent class for ColorMappers.

ColorMapper() - Constructor for class sc.fiji.snt.analysis.ColorMapper

ColorMapReconstructionCmd - Class in sc.fiji.snt.gui.cmds

Implements Reconstruction Viewer's 'Color coding' commands.

ColorMapReconstructionCmd() - Constructor for class sc.fiji.snt.gui.cmds.ColorMapReconstructionCmd

ColorMaps - Class in sc.fiji.snt.util

Utilities for colormaps and IJ lookup tables

ColorMaps() - Constructor for class sc.fiji.snt.util.ColorMaps

COLORMAPS - Static variable in class sc.fiji.snt.viewer.Annotation3D

ColorMenu - Class in sc.fiji.snt.gui

Generates a simplified color widget holding both predetermined colors and user-defined ones.

ColorMenu(String) - Constructor for class sc.fiji.snt.gui.ColorMenu

colorTable - Variable in class sc.fiji.snt.analysis.ColorMapper

colorTagMenu(boolean, Component, Consumer<Color>) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

colorTagMenu(Component, Consumer<Color>) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

colorTagPopup(Component, Consumer<Color>) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

colorTagPresets() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

colorToString(Object) - Static method in class sc.fiji.snt.util.SNTColor

Returns the color encoded as hex string with the format #rrggbbaa.

colorWeight() - Method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Returns the value of the colorWeight record component.

combine(Collection<SNTChart>) - Static method in class sc.fiji.snt.analysis.SNTChart

Combines a collection of charts into a multipanel montage.

combine(Collection<SNTChart>, boolean) - Static method in class sc.fiji.snt.analysis.SNTChart

Combines a collection of charts into a multipanel montage.

combine(Collection<SNTChart>, int, int, boolean) - Static method in class sc.fiji.snt.analysis.SNTChart

Combines a collection of charts into a multipanel montage.

combine(Collection<SNTChart>, String, int, int, boolean) - Static method in class sc.fiji.snt.analysis.SNTChart

Combines a collection of charts into a multipanel montage.

combine(List<Roi>) - Static method in class sc.fiji.snt.analysis.RoiConverter

combine(BoundingBox) - Method in class sc.fiji.snt.util.BoundingBox

Combines this bounding box with another one.

combineAsImagePlus(Collection<SNTChart>) - Static method in class sc.fiji.snt.analysis.SNTChart

Combines a collection of charts into a ImageJ1 stack.

combineCharts() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

combineSkeletons(Collection<Tree>) - Static method in class sc.fiji.snt.util.ImpUtils

combineSkeletons(Collection<Tree>, boolean) - Static method in class sc.fiji.snt.util.ImpUtils

combineSNTChartPrompt() - Method in class sc.fiji.snt.gui.GuiUtils

COMMENTS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

CommonDynamicCmd - Class in sc.fiji.snt.gui.cmds

Command class for GUI commands extending DynamicCommand

CommonDynamicCmd() - Constructor for class sc.fiji.snt.gui.cmds.CommonDynamicCmd

COMPACTNESS_3D - Static variable in class sc.fiji.snt.analysis.ConvexHullAnalyzer

comparator() - Static method in interface sc.fiji.snt.annotation.BrainAnnotation

Comparator - Class in sc.fiji.snt.analysis.sholl.math

Compares two profiles statistically.

Comparator(Profile, Profile) - Constructor for class sc.fiji.snt.analysis.sholl.math.Comparator

CompareFilesCmd - Class in sc.fiji.snt.gui.cmds

Command for opening two SWC/traces files in a dedicated Reconstruction Viewer.

CompareFilesCmd() - Constructor for class sc.fiji.snt.gui.cmds.CompareFilesCmd

compareTo(PlausibilityCheck.Warning) - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCheck.Warning

compareTo(ProfileEntry) - Method in class sc.fiji.snt.analysis.sholl.ProfileEntry

compareTo(NearPoint) - Method in class sc.fiji.snt.NearPoint

compareTo(Path) - Method in class sc.fiji.snt.Path

compareTo(DefaultSearchNode) - Method in class sc.fiji.snt.tracing.DefaultSearchNode

compareTo(SWCPoint) - Method in class sc.fiji.snt.util.SWCPoint

COMPLEXITY_INDEX_ACI - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Complexity index: ACI"

COMPLEXITY_INDEX_DCI - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Complexity index: DCI"

ComponentMover - Class in sc.fiji.snt.gui

This class allows you to move a Component by using a mouse.

ComponentMover() - Constructor for class sc.fiji.snt.gui.ComponentMover

Constructor for moving individual components.

ComponentMover(Component, Component...) - Constructor for class sc.fiji.snt.gui.ComponentMover

Constructor to specify a parent component that will be moved when drag events are generated on a registered child component.

ComponentMover(Class, Component...) - Constructor for class sc.fiji.snt.gui.ComponentMover

Constructor to specify a Class of Component that will be moved when drag events are generated on a registered child component.

ComponentReconnector<T> - Class in sc.fiji.snt.tracing.auto

Bridges gaps between disconnected components of an auto-traced neuron tree.

ComponentReconnector(RandomAccessibleInterval<T>, double[]) - Constructor for class sc.fiji.snt.tracing.auto.ComponentReconnector

Creates a new ComponentReconnector.

computationSettings() - Method in class sc.fiji.snt.NotesUI

compute() - Method in class sc.fiji.snt.analysis.AbstractConvexHull

Computes the convex hull from the input points.

compute() - Method in class sc.fiji.snt.analysis.ConvexHull2D

compute() - Method in class sc.fiji.snt.analysis.ConvexHull3D

compute() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd

compute(ImagePlus, double, String, String) - Static method in class sc.fiji.snt.seed.LabelsToSeeds

Computes one SeedPoint per non-zero label in imp.

compute(Iterator<? extends SNTPoint>) - Method in class sc.fiji.snt.util.BoundingBox

Computes a new positioning so that this box encloses the specified point cloud.

compute(RandomAccessibleInterval<T>, RandomAccessibleInterval<U>) - Method in class sc.fiji.snt.filter.Frangi

compute(RandomAccessibleInterval<T>, RandomAccessibleInterval<U>) - Method in class sc.fiji.snt.filter.SpectralSimilarity

Computes the spectral similarity map.

compute(RandomAccessibleInterval<T>, RandomAccessibleInterval<U>) - Method in class sc.fiji.snt.filter.Tubeness

computeAndApplyScoreMap(DirectedWeightedGraph) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Computes or applies a score map and stamps each graph node's PointInImage.v with its score.

computeAverageRadius(Set<SWCPoint>) - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Computes average radius of a set of nodes.

computeAverageSpacing() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Computes average voxel spacing, handling both 2D and 3D images.

computeBoxivity(AbstractConvexHull) - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

computeCentroid(AbstractConvexHull) - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

computedValue() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCalibrator.CheckSummary

Returns the value of the computedValue record component.

computeEDT(RandomAccessibleInterval<? extends RealType<?>>, int, double[]) - Static method in class sc.fiji.snt.analysis.detection.DetectorUtils

Computes a calibrated Euclidean Distance Transform for a single label value in a label image.

computeElongation(AbstractConvexHull) - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

computeGridSize(double, double, int) - Static method in class sc.fiji.snt.tracing.CrossSectionUtils

Computes the grid size needed to cover a given physical radius at the specified scale, capped to a maximum.

computeGWDT(RandomAccessibleInterval<?>, double, double[], double, double) - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

computeGWDT(RandomAccessibleInterval<?>, double, double[], double, double) - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

computeGWDT(RandomAccessibleInterval<?>, double, double[], double, double) - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Compute Gray-Weighted Distance Transform.

computeGWDT(RandomAccessibleInterval, double, double[], double, double) - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

computeHull(Tree) - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

computeImgStats(Iterable<T>, ImageStatistics) - Method in class sc.fiji.snt.SNT

computeImgStats(Iterable<T>, ImageStatistics, SNT.CostType) - Method in class sc.fiji.snt.SNT

computeIntensityRange() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Computes intensity range for GI normalization.

computeIntensityStats(RandomAccessibleInterval<? extends RealType<?>>) - Static method in class sc.fiji.snt.util.ImgUtils

Computes basic intensity statistics of an image.

computeIntensityWeightedJointCoverage(SWCPoint, RandomAccess<UnsignedShortType>, RandomAccess<? extends RealType<?>>) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Computes INTENSITY-WEIGHTED joint coverage fraction (like APP2).

computeIsotropicScale(double[], double[], double, double, double) - Static method in class sc.fiji.snt.tracing.CrossSectionUtils

Computes the isotropic scale for a cross-section plane given the tangent plane basis vectors and voxel spacing.

computeMaskArea(Img<BitType>, double[]) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Computes the area of a binary mask.

computeMaskCentroid(Img<BitType>, double[]) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Computes the centroid of a binary mask.

computeMeanIntensity(RandomAccessibleInterval<? extends RealType<?>>) - Static method in class sc.fiji.snt.util.ImgUtils

Computes the mean intensity of an image.

computeMinimumThreshold(RandomAccessibleInterval<? extends RealType<?>>) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Computes the Minimum auto-threshold of the given image.

computeNBins(DescriptiveStatistics) - Static method in class sc.fiji.snt.analysis.AnalysisUtils

Computes the "optimal" number of bins for a histogram dataset using Freedman-Diaconis rule.

computeNearestNeighborDistances(List<T>) - Static method in class sc.fiji.snt.analysis.NodeStatistics

Computes nearest neighbor distances.

computeNodeCosts(ImagePlus, Path) - Static method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Computes the cost at each node of a path without modifying it.

computeNodeCosts(ImgPlus<T>, Path) - Static method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Computes the cost at each node of a path without modifying it.

computeOtsuThreshold(RandomAccessibleInterval<? extends RealType<?>>) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Computes Otsu's threshold using ImageJ Ops.

computePercentile(RandomAccessibleInterval<? extends RealType<?>>, double) - Static method in class sc.fiji.snt.util.ImgUtils

Computes an approximate percentile by random sampling.

computePrincipalAxes(String) - Method in class sc.fiji.snt.viewer.OBJMesh

Computes the principal axes of this mesh using the new PCAnalyzer.

COMPUTER_MOUSE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

computeRoundness(AbstractConvexHull) - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

computeScaleAlongVector(double, double, double, double, double, double) - Static method in class sc.fiji.snt.tracing.CrossSectionUtils

Computes the effective physical scale along an arbitrary direction vector given anisotropic voxel spacing.

ComputeSecondaryImg<T,U> - Class in sc.fiji.snt.gui.cmds

Implements the "Generate Secondary Layer" command.

ComputeSecondaryImg() - Constructor for class sc.fiji.snt.gui.cmds.ComputeSecondaryImg

computeTangentPlaneBasis(double, double, double) - Static method in class sc.fiji.snt.tracing.CrossSectionUtils

Computes an orthonormal basis for the plane perpendicular to the given normal (tangent) vector.

computeUprightAngle(Tree, boolean) - Static method in class sc.fiji.snt.util.TreeUtils

Computes the angle (in degrees) needed to make a tree appear upright in the XY viewing plane.

confidence - Variable in class sc.fiji.snt.seed.SeedPoint

Detector confidence in [0, 1].

CONFIDENCE - Enum constant in enum class sc.fiji.snt.seed.SeedOverlay.ColorMode

CONFIDENCE - Enum constant in enum class sc.fiji.snt.tracing.auto.AbstractGWDTTracer.WaypointBiasSource

Bias proportional to each seed's confidence (default).

confidenceRangeFilter() - Method in class sc.fiji.snt.seed.SeedTableModel

Config() - Constructor for class sc.fiji.snt.analysis.detection.AlongPathDetector.Config

Config() - Constructor for class sc.fiji.snt.analysis.detection.LabelProximityDetector.Config

Config() - Constructor for class sc.fiji.snt.analysis.detection.PeripathDetector.Config

Config() - Constructor for class sc.fiji.snt.analysis.PeripathDetector.Config

Deprecated.

Config() - Constructor for class sc.fiji.snt.util.CrossoverFinder.Config

configureCheckboxColumn(JTable, int, String) - Static method in class sc.fiji.snt.gui.GuiUtils.JTables

Configures a Boolean column to render and edit as a checkbox, with an optional header tooltip.

configureSecondaryScoreMap(AbstractGWDTTracer<?>) - Method in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

Hook for configuring the tracer's score map from a user-supplied secondary image.

configureSecondaryScoreMap(AbstractGWDTTracer<?>) - Method in class sc.fiji.snt.plugin.GWDTTracerFileCmd

Locates a paired secondary image on disk via GWDTTracerFileCmd.secondaryImageSuffix.

confirmedSegmentSizes - Variable in class sc.fiji.snt.SNT

confirmIfNotSegmented(ImagePlus) - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

Focused pre-flight for seed-driven subclasses that bypass BinaryTracerCommonCmd.runCommand() (and therefore BinaryTracerCommonCmd.validateBeforeTracing(ij.gui.Roi, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean)).

confirmTemporary(boolean) - Method in class sc.fiji.snt.SNT

confirmTemporarySegments - Variable in class sc.fiji.snt.SNTUI

connectComponents - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

connectedComponents(ImagePlus, boolean) - Static method in class sc.fiji.snt.seed.LabelsToSeeds

Labels the connected components of a binary mask, returning a new labels image suitable for LabelsToSeeds.compute(ImagePlus, double, String, String).

connectedPaths - Variable in class sc.fiji.snt.Path

CONNECTIVITY - Static variable in class sc.fiji.snt.analysis.graph.GraphColorMapper

Flag for "Connected components" mapping.

CONST_8 - Static variable in class sc.fiji.snt.tracing.cost.Reciprocal

constantLUT(Color) - Static method in class sc.fiji.snt.analysis.sholl.ShollUtils

ConstantRadii() - Constructor for class sc.fiji.snt.analysis.curation.PlausibilityCheck.ConstantRadii

contains(BrainAnnotation, BrainAnnotation, boolean) - Method in class sc.fiji.snt.analysis.TreeStatistics

contains(BoundingBox) - Method in class sc.fiji.snt.util.BoundingBox

Checks whether the specified BoundingBox is enclosed by this one .

contains(PointInImage) - Method in class sc.fiji.snt.Path

Check whether this Path contains the specified point

contains(PointInImage, double) - Method in class sc.fiji.snt.Path

Checks if this path contains the specified point within the given tolerance.

contains(SNTPoint) - Method in class sc.fiji.snt.util.BoundingBox

contains2D(SNTPoint) - Method in class sc.fiji.snt.util.BoundingBox

containsUnscaledNodesInViewPort(TracerCanvas) - Method in class sc.fiji.snt.Path

containsValidData() - Method in class sc.fiji.snt.analysis.SNTChart

Checks if the chart contains valid data.

contentAdded(Content) - Method in class sc.fiji.snt.PathAndFillManager

Deprecated.

contentChanged(Content) - Method in class sc.fiji.snt.PathAndFillManager

Deprecated.

contentRemoved(Content) - Method in class sc.fiji.snt.PathAndFillManager

Deprecated.

contentSelected(Content) - Method in class sc.fiji.snt.PathAndFillManager

Deprecated.

context() - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

contour() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Returns the value of the contour record component.

CONTRACTION - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Deprecated.

Use TreeStatistics.BRANCH_CONTRACTION or TreeStatistics.PATH_CONTRACTION instead

contrastColor(Color) - Static method in class sc.fiji.snt.util.SNTColor

Returns a suitable 'contrast' color.

contrastColor(Color) - Static method in class sc.fiji.snt.viewer.Viewer3D.Utils

contrastOptions(JComponent, JComponent, boolean) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

convergenceThreshold() - Method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Returns the value of the convergenceThreshold record component.

convert(Collection<Path>, ImagePlus) - Static method in class sc.fiji.snt.analysis.RoiConverter

convert(RandomAccessible<T>, RandomAccessible<T>) - Method in class sc.fiji.snt.FillConverter

Map values between the input and output at fill voxel positions.

convertBinary(RandomAccessible<T>) - Method in class sc.fiji.snt.FillConverter

Set 1 at fill voxel positions.

convertBranches(Overlay) - Method in class sc.fiji.snt.analysis.RoiConverter

convertBranchPoints() - Method in class sc.fiji.snt.analysis.RoiConverter

Converts all the branch points associated with the parsed paths into PointRois, adding them to the overlay of the image specified in the constructor.

convertBranchPoints(Overlay) - Method in class sc.fiji.snt.analysis.RoiConverter

Converts all the branch points associated with the parsed paths into PointRois

convertDistance(RandomAccessible<T>) - Method in class sc.fiji.snt.FillConverter

Map the node distance measure to fill voxel positions.

convertInnerBranches(Overlay) - Method in class sc.fiji.snt.analysis.RoiConverter

convertInPlaceToCompositeAsNeeded(SNTUI, ImagePlus) - Static method in class sc.fiji.snt.gui.cmds.ChooseDatasetCmd

convertLabels(RandomAccessible<T>) - Method in class sc.fiji.snt.FillConverter

Map the fill component label to fill voxel positions.

convertPaths() - Method in class sc.fiji.snt.analysis.RoiConverter

Converts paths into 2D polyline ROIs (segment paths), adding them to the overlay of the image specified in the constructor.

convertPaths(Overlay) - Method in class sc.fiji.snt.analysis.RoiConverter

Converts paths into 2D polyline ROIs.

convertPaths(Overlay, Collection<Path>) - Method in class sc.fiji.snt.analysis.RoiConverter

Converts an ad-hoc collection of paths into 2D polyline ROIs.

convertPrimaryBranches(Overlay) - Method in class sc.fiji.snt.analysis.RoiConverter

convertRGBtoComposite(ImagePlus) - Static method in class sc.fiji.snt.util.ImpUtils

convertRoots() - Method in class sc.fiji.snt.analysis.RoiConverter

Converts the starting nodes of primary paths in the parsed pool into PointRois

convertRoots(Overlay) - Method in class sc.fiji.snt.analysis.RoiConverter

Converts the starting nodes of primary paths in the parsed pool into PointRois

convertTerminalBranches(Overlay) - Method in class sc.fiji.snt.analysis.RoiConverter

convertTips() - Method in class sc.fiji.snt.analysis.RoiConverter

Converts all the tips associated with the parsed paths into PointRois, adding them to the overlay of the image specified in the constructor.

convertTips(Overlay) - Method in class sc.fiji.snt.analysis.RoiConverter

Converts all the tips associated with the parsed paths into PointRois

convertTo16bit(ImagePlus) - Static method in class sc.fiji.snt.util.ImpUtils

convertTo32bit(ImagePlus) - Static method in class sc.fiji.snt.util.ImpUtils

convertTo8bit(ImagePlus) - Static method in class sc.fiji.snt.util.ImpUtils

convertToSimple2D(ImagePlus, int) - Static method in class sc.fiji.snt.util.ImpUtils

Converts the specified image into an easy displayable form, i.e., a non-composite 2D image If the image is a timelapse, only the first frame is considered; if 3D, a MIP is retrieved; if multichannel, an RGB version is obtained.

convertValueToString(Object) - Method in class sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter

convertValueToString(Object) - Method in class sc.fiji.snt.viewer.geditor.SNTPseudographAdapter

convertValueToString(Object) - Method in class sc.fiji.snt.viewer.geditor.TreeGraphAdapter

CONVEX_HULL_BOUNDARY_SIZE - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Convex hull: Boundary size" statistics

CONVEX_HULL_BOXIVITY - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Convex hull: Boxivity" statistics

CONVEX_HULL_CENTROID_ROOT_DISTANCE - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Convex hull: Centroid-root distance" statistics

CONVEX_HULL_COMPACTNESS_3D - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Convex hull: Compactness" statistics

CONVEX_HULL_ECCENTRICITY_2D - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Convex hull: Eccentricity" statistics

CONVEX_HULL_ELONGATION - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Convex hull: Elongation" statistics

CONVEX_HULL_ROUNDNESS - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Convex hull: Roundness" statistics

CONVEX_HULL_SIZE - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Convex hull: Size" statistics

convexHull() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

ConvexHull2D - Class in sc.fiji.snt.analysis

Computes the convex hull of a set of 2D points.

ConvexHull2D(Collection<T>) - Constructor for class sc.fiji.snt.analysis.ConvexHull2D

ConvexHull2D(Context, Collection<T>) - Constructor for class sc.fiji.snt.analysis.ConvexHull2D

ConvexHull3D - Class in sc.fiji.snt.analysis

Convex hull analysis in 3D.

ConvexHull3D(Collection<T>) - Constructor for class sc.fiji.snt.analysis.ConvexHull3D

ConvexHull3D(Context, Collection<T>) - Constructor for class sc.fiji.snt.analysis.ConvexHull3D

ConvexHullAnalyzer - Class in sc.fiji.snt.analysis

Class for Convex Hull measurements of a Tree.

ConvexHullAnalyzer(AbstractConvexHull) - Constructor for class sc.fiji.snt.analysis.ConvexHullAnalyzer

Instantiates a new convex hull analyzer.

ConvexHullAnalyzer(Tree) - Constructor for class sc.fiji.snt.analysis.ConvexHullAnalyzer

Instantiates a new convex hull analyzer.

ConvexHullCmd - Class in sc.fiji.snt.plugin

Implements the "Convex Hull Analysis..." command.

ConvexHullCmd() - Constructor for class sc.fiji.snt.plugin.ConvexHullCmd

copy() - Method in class sc.fiji.snt.util.CircleCursor3D

copy() - Method in class sc.fiji.snt.util.DiskCursor3D

copy() - Method in class sc.fiji.snt.util.PathCursor

COPY - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

copySelectionToClipboard() - Method in class sc.fiji.snt.gui.OntologyBrowser

Copies the checked terms to the system clipboard.

copyToClipboard(JTable, boolean) - Static method in class sc.fiji.snt.gui.GuiUtils.JTables

Core Classes - Search tag in package sc.fiji.snt.tracing

Section

COS_SIMILARITY_KEY - Static variable in class sc.fiji.snt.gui.cmds.MultiSpectralRefinerCmd

cosSimilarityThreshold() - Method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Returns the value of the cosSimilarityThreshold record component.

Cost - Interface in sc.fiji.snt.tracing.cost

Interface for cost function implementations used by SearchInterface

costFunction - Variable in class sc.fiji.snt.tracing.BiSearch

costFunction - Variable in class sc.fiji.snt.tracing.SearchThread

costFunctionPicked(SNT.CostType, Path) - Method in interface sc.fiji.snt.gui.CostPalette.Listener

User picked a CostType; chosenPath is the corresponding A* result.

CostFunctionSelectionCmd - Class in sc.fiji.snt.gui.cmds

Entry-point command for the cost-function wizard.

CostFunctionSelectionCmd() - Constructor for class sc.fiji.snt.gui.cmds.CostFunctionSelectionCmd

costMovingTo(double) - Method in interface sc.fiji.snt.tracing.cost.Cost

costMovingTo(double) - Method in class sc.fiji.snt.tracing.cost.Difference

costMovingTo(double) - Method in class sc.fiji.snt.tracing.cost.DifferenceSq

costMovingTo(double) - Method in class sc.fiji.snt.tracing.cost.OneMinusErf

costMovingTo(double) - Method in class sc.fiji.snt.tracing.cost.Reciprocal

CostPalette - Class in sc.fiji.snt.gui

SNT "Cost Function Wizard": runs A* with each of the SNT.CostType variants between two endpoints and displays all candidate paths as colored overlays on a single cropped ImagePlus.

CostPalette(SNT, PointInImage, PointInImage) - Constructor for class sc.fiji.snt.gui.CostPalette

CostPalette.Listener - Interface in sc.fiji.snt.gui

Listener notified when the user picks (or cancels).

count - Variable in class sc.fiji.snt.analysis.sholl.ProfileEntry

The number of intersection counts associated at this entry's radius

COUNT - Static variable in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

countDescendants(Path) - Static method in class sc.fiji.snt.util.TreeUtils

Counts all descendants (children, grandchildren, etc.) of a path.

countOutOfBounds(long[], double[]) - Method in class sc.fiji.snt.seed.SeedOverlay

Counts seeds whose voxel coordinates fall outside the given image bounds.

counts() - Method in class sc.fiji.snt.analysis.sholl.Profile

countsAsArray() - Method in class sc.fiji.snt.analysis.sholl.Profile

create(ImagePlus) - Static method in class sc.fiji.snt.tracing.auto.DiskBackedGWDTTracer

create(ImagePlus) - Static method in class sc.fiji.snt.tracing.auto.GWDTTracer

create(ImagePlus) - Static method in class sc.fiji.snt.tracing.auto.GWDTTracerFactory

Creates the optimal GWDT tracer from an ImagePlus.

create(ImagePlus) - Static method in class sc.fiji.snt.tracing.auto.SparseGWDTTracer

create(String, int, int, int, int) - Static method in class sc.fiji.snt.util.ImpUtils

create(ImgPlus<?>) - Static method in class sc.fiji.snt.tracing.auto.DiskBackedGWDTTracer

create(ImgPlus<?>) - Static method in class sc.fiji.snt.tracing.auto.GWDTTracer

create(ImgPlus<?>) - Static method in class sc.fiji.snt.tracing.auto.GWDTTracerFactory

Creates the optimal GWDT tracer from an ImgPlus.

create(ImgPlus<?>) - Static method in class sc.fiji.snt.tracing.auto.SparseGWDTTracer

create(RandomAccessibleInterval<?>, double[]) - Static method in class sc.fiji.snt.tracing.auto.GWDTTracerFactory

Creates the optimal GWDT tracer for the given image.

create(RandomAccessibleInterval<?>, double[], long, long) - Static method in class sc.fiji.snt.tracing.auto.GWDTTracerFactory

Creates optimal tracer with manual threshold override.

create(BiSearch) - Method in class sc.fiji.snt.tracing.artist.SearchArtistFactory

Creates a BiSearchArtist for the specified BiSearch.

create(FillerThread) - Method in class sc.fiji.snt.tracing.artist.SearchArtistFactory

Creates a FillerThreadArtist for the specified FillerThread.

create(SearchInterface) - Method in class sc.fiji.snt.tracing.artist.SearchArtistFactory

Creates a SearchArtist for the specified search interface.

create(TracerThread) - Method in class sc.fiji.snt.tracing.artist.SearchArtistFactory

Creates a SearchThreadArtist for the specified TracerThread.

createAndConfigureConverter(ImagePlus, ImagePlus) - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

Builds and configures a BinaryTracer for the supplied images.

createAndConfigureTracer(ImgPlus<?>) - Method in class sc.fiji.snt.plugin.AutotraceFromTipsCmd

Extends the parent's tracer setup with a setTips call.

createAndConfigureTracer(ImgPlus<?>) - Method in class sc.fiji.snt.plugin.AutotraceFromWaypointsCmd

Extends the parent's tracer setup with bias configuration and a setWaypoints call.

createAndConfigureTracer(ImgPlus<?>) - Method in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

Creates and configures a tracer from the shared GUI parameters.

createAnnotationGraph() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

createCanvas() - Method in class sc.fiji.snt.viewer.geditor.AnnotationGraphComponent

createCanvas() - Method in class sc.fiji.snt.viewer.geditor.SNTPseudographComponent

createCanvas(ImagePlus, int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

createCanvas(ImagePlus, int) - Method in class sc.fiji.snt.SNT

createCircleRoi() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Creates a circular ROI using the estimated radius.

createCircles() - Method in class sc.fiji.snt.Path

Deprecated.

No longer needed - radii and tangents are now stored per-node

createCloseButton(AbstractAction) - Method in class sc.fiji.snt.gui.SNTSearchableBar

createContourRoi() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Creates a polygon ROI from the contour.

createDefaultPopupMenu() - Method in class sc.fiji.snt.gui.OntologyBrowser.OntologyTab

Creates the default popup menu with generic tree navigation actions: Deselect All, Uncheck All, Collapse/Expand All, Collapse/Expand Selected Level, and Auto-select Children toggle.

createDendrogram() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

createFindNextButton(AbstractAction) - Method in class sc.fiji.snt.gui.SNTSearchableBar

createFindPrevButton(AbstractAction) - Method in class sc.fiji.snt.gui.SNTSearchableBar

createFrame(Context) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

createFromFile(String, int...) - Static method in class sc.fiji.snt.PathAndFillManager

Creates a PathAndFillManager instance from imported data

createFromGraph(DirectedWeightedGraph, boolean) - Static method in class sc.fiji.snt.PathAndFillManager

Create a new PathAndFillManager instance from the graph.

createFromNodes(Collection<SWCPoint>) - Static method in class sc.fiji.snt.PathAndFillManager

Creates a PathAndFillManager instance from a collection of reconstruction nodes.

createGraph(Collection<SWCPoint>, boolean) - Static method in class sc.fiji.snt.analysis.graph.GraphUtils

Deprecated.

createGraph(Tree) - Static method in class sc.fiji.snt.analysis.graph.GraphUtils

Deprecated.

createHighlightButton() - Method in class sc.fiji.snt.gui.SNTSearchableBar

createImg(Interval, int[], T, CellLoader<T>) - Static method in class sc.fiji.snt.filter.Lazy

createIntervals(long[], long[]) - Static method in class sc.fiji.snt.util.ImgUtils

Partition the source dimensions into a list of Intervals with given dimensions.

createIsotropicSpacing(int) - Static method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

createLayout(String) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

Creates a layout instance for the given identifier.

createNewNode(int, int, int, double, double, DefaultSearchNode, byte) - Method in class sc.fiji.snt.tracing.SearchThread

createOrUpdateDisplay() - Method in class sc.fiji.snt.analysis.SNTTable

Creates a new display or updates an existing one.

createPath() - Method in class sc.fiji.snt.Path

Returns a new Path with this Path's attributes (e.g. spatial scale), but no nodes.

createPointRoi() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Creates a point ROI at the soma center.

createStatusBar() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

createStorageBackend() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Create the storage backend for this tracer.

createStorageBackend() - Method in class sc.fiji.snt.tracing.auto.DiskBackedGWDTTracer

createStorageBackend() - Method in class sc.fiji.snt.tracing.auto.GWDTTracer

createStorageBackend() - Method in class sc.fiji.snt.tracing.auto.SparseGWDTTracer

createSupplier(SNT.SearchImageType, Class<V>, int, int) - Static method in class sc.fiji.snt.tracing.image.SupplierUtil

createTimeline(Map<String, List<GrowthAnalyzer.GrowthPhase>>, String) - Static method in class sc.fiji.snt.analysis.AnalysisUtils

Creates a horizontal timeline chart with one row per neurite showing color-coded growth phases in sequence, so that each neurite gets one row with colored segments representing different phases.

createToolBar() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

createTorusMask(Collection<Path>, ImagePlus, PeripathDetector.Config, double) - Static method in class sc.fiji.snt.analysis.detection.PeripathDetector

Creates a binary torus mask around the given paths, writing into an ImagePlus.

createTorusMask(Collection<Path>, ImagePlus, PeripathDetector.Config, double) - Static method in class sc.fiji.snt.analysis.PeripathDetector

Deprecated.

Use PeripathDetector.createTorusMask(java.util.Collection<sc.fiji.snt.Path>, net.imglib2.RandomAccessibleInterval<T>, sc.fiji.snt.analysis.detection.PeripathDetector.Config, double) instead.

createTorusMask(Collection<Path>, RandomAccessibleInterval<T>, PeripathDetector.Config, double) - Static method in class sc.fiji.snt.analysis.detection.PeripathDetector

Creates a binary torus mask around the given paths.

createTorusMask(Collection<Path>, RandomAccessibleInterval<T>, PeripathDetector.Config, double) - Static method in class sc.fiji.snt.analysis.PeripathDetector

Deprecated.

Use PeripathDetector.createTorusMask(java.util.Collection<sc.fiji.snt.Path>, net.imglib2.RandomAccessibleInterval<T>, sc.fiji.snt.analysis.detection.PeripathDetector.Config, double) instead.

createTree(String, int, int, double, int) - Method in class sc.fiji.snt.util.LSystemsTree

createTree(Graph<SWCPoint, ?>) - Static method in class sc.fiji.snt.analysis.graph.GraphUtils

Deprecated.

createTreeStack(String) - Method in class sc.fiji.snt.util.LSystemsTree

createUndoManager() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

crop(ImagePlus, Number) - Static method in class sc.fiji.snt.util.ImpUtils

Crops the image around non-background values.

crop(ImgPlus<T>, long[], long[], boolean) - Static method in class sc.fiji.snt.util.ImgUtils

Crop a region from an ImgPlus using (x, y, z) pixel coordinates.

crop(ImgPlus<T>, long[], long[], long, boolean) - Static method in class sc.fiji.snt.util.ImgUtils

Crop a region from an ImgPlus using (x, y, z) pixel coordinates.

crop(ImgPlus<T>, long[], long[], long, boolean, boolean) - Static method in class sc.fiji.snt.util.ImgUtils

Crop a region from an ImgPlus using (x, y, z) pixel coordinates.

crop(RandomAccessibleInterval<T>, long[], long[], long) - Static method in class sc.fiji.snt.util.ImgUtils

Crop a region from a RandomAccessibleInterval using (x, y, z) pixel coordinates.

CROSSHAIR - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

CrossoverFinder - Class in sc.fiji.snt.util

Utility to detect crossover locations between paths: spatially close locations between paths that look like intersections in the image but are not topological joins in the traced graph.

CrossoverFinder() - Constructor for class sc.fiji.snt.util.CrossoverFinder

CrossoverFinder.Config - Class in sc.fiji.snt.util

Immutable configuration with builder-like setters.

CrossoverFinder.CrossoverEvent - Class in sc.fiji.snt.util

One detected crossover event.

CrossSectionUtils - Class in sc.fiji.snt.tracing

Static utilities for computing cross-sectional planes perpendicular to a path tangent.

CSV - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

csvQuoteAndPrint(PrintWriter, Object) - Static method in class sc.fiji.snt.SNTUtils

csvSample() - Static method in class sc.fiji.snt.analysis.sholl.ShollUtils

CT_UNSET - Static variable in class sc.fiji.snt.seed.SeedPoint

Sentinel for missing/unspecified channel or frame.

ctPositionChanged() - Method in class sc.fiji.snt.SNTUI

ctrlKey() - Static method in class sc.fiji.snt.gui.GuiUtils

CUBE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

CUBES - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

cullSingleNodePaths - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

CURATION_EXTENSION - Static variable in class sc.fiji.snt.analysis.curation.PlausibilityCalibrator

The file extension for curation preset files (without leading dot).

CurationManager - Class in sc.fiji.snt

Implements the Curation Assistant pane in SNT's UI.

CurationManager(SNTUI, PlausibilityMonitor) - Constructor for class sc.fiji.snt.CurationManager

CurationTags - Class in sc.fiji.snt.analysis.curation

Reserved cur:* path tags used to record a path's review status after it has been examined in the Curation Assistant.

CurationTags.Partition - Record Class in sc.fiji.snt.analysis.curation

Four-bucket breakdown returned by CurationTags.partitionByReviewStatus(Tree).

currentFile - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor

currentPath - Variable in class sc.fiji.snt.SNT

cursorLocked - Variable in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

cursorSnapWindowXY - Variable in class sc.fiji.snt.SNT

cursorSnapWindowZ - Variable in class sc.fiji.snt.SNT

CustomizeAxesCmd - Class in sc.fiji.snt.gui.cmds

Command for customizing axis-to-anatomy mappings in Reconstruction Viewer.

CustomizeAxesCmd() - Constructor for class sc.fiji.snt.gui.cmds.CustomizeAxesCmd

CustomizeLegendCmd - Class in sc.fiji.snt.gui.cmds

Command for customizing a LUT legend in Reconstruction Viewer

CustomizeLegendCmd() - Constructor for class sc.fiji.snt.gui.cmds.CustomizeLegendCmd

CustomizeObjCmd - Class in sc.fiji.snt.gui.cmds

Command for customizing an OBJ mesh in Reconstruction Viewer

CustomizeObjCmd() - Constructor for class sc.fiji.snt.gui.cmds.CustomizeObjCmd

CustomizeTreeCmd - Class in sc.fiji.snt.gui.cmds

Command for customizing selected Trees in Reconstruction Viewer.

CustomizeTreeCmd() - Constructor for class sc.fiji.snt.gui.cmds.CustomizeTreeCmd

CUT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

CV - Enum constant in enum class sc.fiji.snt.analysis.ProfileProcessor.Metric

D

d2s(double) - Static method in class sc.fiji.snt.analysis.sholl.ShollUtils

DANGER - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

darkNodeAndSegmentPruning(DirectedWeightedGraph, double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

APP2-style dark node and segment pruning.

DATABASE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

dCam - Variable in class sc.fiji.snt.viewer.Bvv.Keyframe

Camera depth parameter (perspective).

debug(Object) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

debug(Object) - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

debug(Object) - Method in class sc.fiji.snt.util.Logger

Logs a debug message (only if debug mode is enabled).

debugMode - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

debugMode - Variable in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

debugMode() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

DECAY - Static variable in class sc.fiji.snt.analysis.ShollAnalyzer

deduplicate(List<Detection>, double) - Static method in class sc.fiji.snt.analysis.detection.DetectorUtils

Deduplicates detections using greedy non-maximum suppression by intensity.

DeepCheck() - Constructor for class sc.fiji.snt.analysis.curation.PlausibilityCheck.DeepCheck

DEF_ANGLE_STEP_SIZE - Static variable in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

Default angle step size for Polar analyses

DEF_ANIMATION_MODE - Static variable in class sc.fiji.snt.gui.cmds.RecViewerPrefsCmd

Default animation mode for 3D viewer rotations

DEF_CONTROLS_SENSITIVITY - Static variable in class sc.fiji.snt.gui.cmds.RecViewerPrefsCmd

Default sensitivity setting for 3D viewer controls

DEF_DEBUG_MODE - Static variable in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

DEF_DETAILED_METRICS - Static variable in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

DEF_ENCLOSING_RADIUS_CUTOFF - Static variable in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

Default cutoff value for enclosing radius

DEF_INCLUDE_ZERO_COUNTS - Static variable in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

Default setting for including zero counts in analysis

DEF_KS_TESTING - Static variable in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

DEF_MAX_DEGREE - Static variable in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

Default maximum degree for polynomial fitting

DEF_MIN_DEGREE - Static variable in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

Default minimum degree for polynomial fitting

DEF_NODE_RADIUS - Static variable in class sc.fiji.snt.viewer.Viewer3D

DEF_ROI_SIZE - Static variable in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

DEF_ROTATION_ANGLE - Static variable in class sc.fiji.snt.gui.cmds.RecViewerPrefsCmd

Default rotation angle for 3D viewer animations (360 degrees)

DEF_ROTATION_DURATION - Static variable in class sc.fiji.snt.gui.cmds.RecViewerPrefsCmd

Default rotation duration for 3D viewer animations (12 seconds)

DEF_ROTATION_FPS - Static variable in class sc.fiji.snt.gui.cmds.RecViewerPrefsCmd

Default frames per second for 3D viewer animations

DEF_RSQUARED - Static variable in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

DEF_SCRIPT_EXTENSION - Static variable in class sc.fiji.snt.gui.cmds.RecViewerPrefsCmd

Default file extension for scripts

DEF_SKIP_SINGLE_VOXELS - Static variable in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

Default setting for skipping single voxel intersections

DEF_SKIP_SOMATIC_SEGMENTS - Static variable in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

Default setting for skipping somatic segments

DEF_SNAPSHOT_DIR - Static variable in class sc.fiji.snt.gui.cmds.RecViewerPrefsCmd

DEF_SNAPSHOT_WYSIWYG - Static variable in class sc.fiji.snt.gui.cmds.RecViewerPrefsCmd

Default WYSIWYG snapshot mode (off: use GL readback)

DEFAULT - Enum constant in enum class sc.fiji.snt.viewer.Viewer3D.ViewMode

No enforcement of view point: freely turn around the scene.

DEFAULT_ABSOLUTE_WINDOW_SIZE - Static variable in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Default absolute window size in frames (used when useAbsoluteWindowSize is true)

DEFAULT_BASE_THRESHOLD_FRACTION - Static variable in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Default base threshold as fraction of overall growth rate for PLATEAU/LAG classification

DEFAULT_COLOR_TABLE_NAME - Static variable in class sc.fiji.snt.seed.SeedOverlay

Default LUT name (resolved via ColorMaps.get(String)).

DEFAULT_DESELECTED_COLOR - Static variable in class sc.fiji.snt.SNT

DEFAULT_DESELECTED_COLOR3F - Static variable in class sc.fiji.snt.SNT

DEFAULT_MIN_ANGLE - Static variable in class sc.fiji.snt.PathFitter

The default value for the smallest angle (in radians) constraining the fit.

DEFAULT_MIN_PATH_LENGTH - Static variable in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Default minimum path length for analysis

DEFAULT_MIN_TIME_POINTS - Static variable in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Default minimum time points required for analysis

DEFAULT_PERCENT - Static variable in class sc.fiji.snt.gui.GuiUtils.JTables.VisitingZoom

DEFAULT_PHASE_SENSITIVITY - Static variable in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Default phase detection sensitivity (0.05-1.0 range, higher = more sensitive)

DEFAULT_RAPID_THRESHOLD_MULTIPLE - Static variable in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Default rapid growth threshold as multiple of overall growth rate for RAPID classification

DEFAULT_RETRACTION_THRESHOLD - Static variable in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Default retraction threshold percentage

DEFAULT_SAMPLING_INTERVAL - Static variable in class sc.fiji.snt.Path

DEFAULT_SEARCH_RADIUS_PIXELS - Static variable in class sc.fiji.snt.gui.cmds.PathFitterCmd

The default search radius constraining the fit (in pixels).

DEFAULT_SELECTED_COLOR - Static variable in class sc.fiji.snt.SNT

DEFAULT_SELECTED_COLOR3F - Static variable in class sc.fiji.snt.SNT

DEFAULT_USE_ABSOLUTE_WINDOW_SIZE - Static variable in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Default setting for using absolute window size instead of fraction

DEFAULT_USE_GLOBAL_THRESHOLDS - Static variable in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Default setting for using global mean growth rate for thresholds

DEFAULT_WINDOW_SIZE_FRACTION - Static variable in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Default window size fraction for change point detection

defaultColor() - Static method in class sc.fiji.snt.gui.IconFactory

defaultGbc() - Static method in class sc.fiji.snt.gui.GuiUtils

defaultHeight() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

defaultPercentageFor(ImagePlus) - Method in class sc.fiji.snt.gui.GuiUtils.JTables.VisitingZoom

defaults() - Static method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Default parameters: weights and thresholds from the nCorrect publication, with intensity thresholds set to NaN (auto-calibrated from bit depth).

DefaultSearchNode - Class in sc.fiji.snt.tracing

A SearchNode which can maintain both a from-start and from-goal search state.

DefaultSearchNode() - Constructor for class sc.fiji.snt.tracing.DefaultSearchNode

DefaultSearchNode(int, int, int, double, double, DefaultSearchNode, byte) - Constructor for class sc.fiji.snt.tracing.DefaultSearchNode

defaultXtitle(Profile) - Static method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

delete(Color) - Static method in class sc.fiji.snt.gui.GuiUtils.Buttons

DELETE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

deleteFills(int[]) - Method in class sc.fiji.snt.PathAndFillManager

deletePath(int) - Method in class sc.fiji.snt.PathAndFillManager

Deletes a Path by index

deletePath(Path) - Method in class sc.fiji.snt.PathAndFillManager

Deletes a path.

deletePaths(int[]) - Method in class sc.fiji.snt.PathAndFillManager

Delete paths by position.

deletePaths(Collection<Path>) - Method in class sc.fiji.snt.PathAndFillManager

Deletes a collection of paths.

DelineationsManager - Class in sc.fiji.snt

Implements the Delineation Analysis pane.

DelineationsManager(SNTUI) - Constructor for class sc.fiji.snt.DelineationsManager

demo(String) - Static method in class sc.fiji.snt.util.ImpUtils

Returns one of the demo images bundled with SNT image associated with the demo (fractal) tree.

DEMO_SCRIPT - Static variable in class sc.fiji.snt.gui.ScriptInstaller

Pattern to match demo scripts (case-insensitive)

demoImage(String) - Method in class sc.fiji.snt.SNTService

Returns one of the demo images bundled with SNT image associated with the demo (fractal) tree.

demoImg(String) - Method in class sc.fiji.snt.SNTService

Returns one of the demo images bundled with SNT as an ImgPlus.

demoProfile() - Static method in class sc.fiji.snt.analysis.sholl.ShollUtils

DemoRunner - Class in sc.fiji.snt.gui

Manages loading and running of demonstration datasets and reconstructions in SNT.

DemoRunner(Context) - Constructor for class sc.fiji.snt.gui.DemoRunner

DemoRunner(SNTUI, SNT) - Constructor for class sc.fiji.snt.gui.DemoRunner

DemoRunner.Demo - Class in sc.fiji.snt.gui

demoTree() - Method in class sc.fiji.snt.SNTService

Deprecated.

demoTree(String) - Method in class sc.fiji.snt.SNTService

Returns a demo tree.

demoTreeImage() - Method in class sc.fiji.snt.SNTService

Deprecated.

demoTrees() - Static method in class sc.fiji.snt.io.MouseLightLoader

Returns a collection of four demo reconstructions NB: Data is cached locally.

demoTrees() - Method in class sc.fiji.snt.SNTService

Returns a collection of four demo reconstructions (dendrites from pyramidal cells from the MouseLight database).

demoTreesSWC() - Method in class sc.fiji.snt.SNTService

DENDRITE - Static variable in class sc.fiji.snt.io.MouseLightLoader

The Constant DENDRITE.

DENDRITIC - Static variable in interface sc.fiji.snt.TreeProperties

depth - Variable in class sc.fiji.snt.gui.cmds.AnnotationGraphGeneratorCmd

depth - Variable in class sc.fiji.snt.gui.cmds.NewGraphOptionsCmd

depth - Variable in class sc.fiji.snt.SNT

depth() - Method in class sc.fiji.snt.annotation.AllenCompartment

depth() - Method in class sc.fiji.snt.util.BoundingBox

DEPTH - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Depth"

deregisterComponent(Component...) - Method in class sc.fiji.snt.gui.ComponentMover

Remove listeners from the specified component

DESCRIPTION_HTML - Static variable in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

deselectedColor - Variable in class sc.fiji.snt.SNT

deselectedColor3f - Variable in class sc.fiji.snt.SNT

deselectSelectAllMenuItem(JTable, Runnable) - Static method in class sc.fiji.snt.gui.GuiUtils.JTables

Common "Deselect / Select All" toggle menu item.

detach() - Method in class sc.fiji.snt.gui.GuiUtils.JTables.DetachableTable

Detaches into a floating dialog.

DetachableTable(JScrollPane, String, Runnable) - Constructor for class sc.fiji.snt.gui.GuiUtils.JTables.DetachableTable

DetachableTable(JScrollPane, String, Runnable, Dimension) - Constructor for class sc.fiji.snt.gui.GuiUtils.JTables.DetachableTable

detachFromParent() - Method in class sc.fiji.snt.Path

Detaches this path from its parent, converting it into an independent primary path.

detailReport(SNTTable) - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Writes PolarProfileStats.Report details to a table.

detect(Collection<Path>, RandomAccessibleInterval<? extends RealType<?>>, AlongPathDetector.Config) - Static method in class sc.fiji.snt.analysis.detection.AlongPathDetector

Detects swellings (boutons/varicosities) along the given paths by analyzing the longitudinal radius profile and, optionally, on-skeleton image intensity.

detect(Collection<Path>, RandomAccessibleInterval<? extends RealType<?>>, LabelProximityDetector.Config) - Static method in class sc.fiji.snt.analysis.detection.LabelProximityDetector

Detects proximity contacts between paths and labeled surfaces.

detect(Collection<Path>, RandomAccessibleInterval<? extends RealType<?>>, PeripathDetector.Config) - Static method in class sc.fiji.snt.analysis.detection.PeripathDetector

Detects intensity maxima along the given paths.

detect(Collection<Path>, RandomAccessibleInterval<? extends RealType<?>>, PeripathDetector.Config) - Static method in class sc.fiji.snt.analysis.PeripathDetector

Deprecated.

Use PeripathDetector.detect(java.util.Collection<sc.fiji.snt.Path>, net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>>, sc.fiji.snt.analysis.detection.PeripathDetector.Config) instead.

detect(Collection<Path>, AlongPathDetector.Config) - Static method in class sc.fiji.snt.analysis.detection.AlongPathDetector

Convenience overload that performs radius-only detection (no image).

detectAllSomas(ImgPlus<?>) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Detects all somas using ImgPlus with default settings.

detectAllSomas(ImgPlus<?>, double, int, double) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Detects all somas using ImgPlus with automatic spacing.

detectAllSomas(ImgPlus<?>, double, int, double, double) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Detects all somas using ImgPlus with automatic spacing and NMS.

detectAllSomas(RandomAccessibleInterval<? extends RealType<?>>, double) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Detects all somas using default minimum radius.

detectAllSomas(RandomAccessibleInterval<? extends RealType<?>>, double, double) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Detects all somas using EDT local maxima approach.

detectAllSomas(RandomAccessibleInterval<? extends RealType<?>>, double, double, double) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Detects all somas in a 2D image using EDT + local maxima + NMS.

detectEditingPath() - Method in class sc.fiji.snt.SNT

Detection - Class in sc.fiji.snt.analysis.detection

One detected feature along or around a traced path (varicosity, spine, bouton, punctum, etc.).

Detection(double, double, double, double, Path, int, double) - Constructor for class sc.fiji.snt.analysis.detection.Detection

Creates a new detection.

Detection(double, double, double, double, Path, int, double) - Constructor for class sc.fiji.snt.analysis.PeripathDetector.Detection

Deprecated.

Detection(double, double, double, double, Path, int, double, int) - Constructor for class sc.fiji.snt.analysis.detection.Detection

Creates a new detection with an associated label value.

detectLayout(String) - Static method in class sc.fiji.snt.io.OmeAxisUtils

Detect the OME-ZARR layout type for a local path.

DetectorUtils - Class in sc.fiji.snt.analysis.detection

Shared utilities for path-based detectors (PeripathDetector, AlongPathDetector).

detectSoma(ImgPlus<?>) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Full soma detection using ImgPlus with automatic thresholding.

detectSoma(ImgPlus<?>, double, int) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Full soma detection using ImgPlus with spacing extracted automatically.

detectSoma(RandomAccessibleInterval<? extends RealType<?>>, double, double[]) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Full soma detection: finds center, floods region, extracts contour.

detectSomaAt(ImgPlus<?>, long, long, double, int) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Detects soma at a specific seed point using ImgPlus.

detectSomaAt(RandomAccessibleInterval<? extends RealType<?>>, long, long, double) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Detects soma at a specific seed point.

detectSomasAt(ImagePlus, Collection<Roi>) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Detects somas at the centroids of the given ROIs.

detectSomasAt(ImgPlus<?>, List<long[]>) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Detects somas at the given seed coordinates using an ImgPlus.

detectSomasAt(RandomAccessibleInterval<? extends RealType<?>>, List<long[]>) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Detects somas at the given seed coordinates.

devResourceJavaAPI() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

devResourceMain() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

devResourcePythonAPI() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

DIAGRAM - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

dialog(String, JComponent, String) - Method in class sc.fiji.snt.gui.GuiUtils

dialogItemChanged(GenericDialog, AWTEvent) - Method in class sc.fiji.snt.plugin.ij1.Strahler

DICE_20 - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

difference(AnnotationGraph, AnnotationGraph) - Static method in class sc.fiji.snt.analysis.graph.AnnotationGraphUtils

Return the graph representing the difference of edge sets of graph1 - graph2

Difference - Class in sc.fiji.snt.tracing.cost

Cost function that computes path cost based on the difference between voxel values and a specified range, useful for tracing along intensity gradients.

Difference(double, double) - Constructor for class sc.fiji.snt.tracing.cost.Difference

DIFFERENCE - Enum constant in enum class sc.fiji.snt.SNT.CostType

DIFFERENCE_SQUARED - Enum constant in enum class sc.fiji.snt.SNT.CostType

DifferenceSq - Class in sc.fiji.snt.tracing.cost

DifferenceSq(double, double) - Constructor for class sc.fiji.snt.tracing.cost.DifferenceSq

Dijkstra - Class in sc.fiji.snt.tracing.heuristic

A Heuristic that always returns zero, reducing A* search to Dijkstra's algorithm.

Dijkstra() - Constructor for class sc.fiji.snt.tracing.heuristic.Dijkstra

DIJKSTRA - Enum constant in enum class sc.fiji.snt.SNT.HeuristicType

dimensionOrder() - Method in record class sc.fiji.snt.io.OmeAxisUtils.OmeMetadata

Returns the value of the dimensionOrder record component.

dims - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

DirectedWeightedGraph - Class in sc.fiji.snt.analysis.graph

Class for accessing a reconstruction as a graph structure.

DirectedWeightedGraph() - Constructor for class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Creates an empty DirectedWeightedGraph.

DirectedWeightedGraph(Collection<SWCPoint>, boolean) - Constructor for class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Creates a DirectedWeightedGraph from a collection of reconstruction nodes.

DirectedWeightedGraph(Supplier<SWCPoint>, Supplier<SWCWeightedEdge>, GraphType, GraphSpecificsStrategy<SWCPoint, SWCWeightedEdge>) - Constructor for class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Subclass hook for installing a custom GraphSpecificsStrategy.

DirectedWeightedGraph(Tree) - Constructor for class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Creates a DirectedWeightedGraph from a Tree with edge weights corresponding to inter-node distances.

DirectedWeightedGraph(Tree, boolean) - Constructor for class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Creates a DirectedWeightedGraph from a Tree, with the option to assign edge weights corresponding to inter-node distances.

DirectedWeightedSubgraph - Class in sc.fiji.snt.analysis.graph

Class for accessing the sub-graph that has a subset of vertices and a subset of edges of a DirectedWeightedGraph.

DirectedWeightedSubgraph(DirectedWeightedGraph, Set<SWCPoint>) - Constructor for class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph

Creates a subgraph from a sub-set of nodes.

DIRECTIONAL - Enum constant in enum class sc.fiji.snt.analysis.CircularModels.Domain

DirectionContinuity() - Constructor for class sc.fiji.snt.analysis.curation.PlausibilityCheck.DirectionContinuity

directionPeaks() - Method in record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.Report

Returns the value of the directionPeaks record component.

disableEdgeStyle - Variable in class sc.fiji.snt.gui.cmds.mxOrganicLayoutPrefsCmd

Specifies if the STYLE_NOEDGESTYLE flag should be set on edges that are modified by the result.

disableEvents(boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Sets whether mouse and key events should be waived back to IJ.

disableEventsAllPanes(boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

disableImageDependentComponents() - Method in class sc.fiji.snt.SNTUI

disableZoomAllPanes(boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

discardFill() - Method in class sc.fiji.snt.SNT

discardFit() - Method in class sc.fiji.snt.Path

discardOnDoubleCancellation - Variable in class sc.fiji.snt.SNTUI

disconnectFromAll() - Method in class sc.fiji.snt.Path

discreteColors(ColorTable, int) - Static method in class sc.fiji.snt.util.ColorMaps

discreteColorsAWT(ColorTable, int) - Static method in class sc.fiji.snt.util.ColorMaps

discreteMsg(String) - Method in class sc.fiji.snt.SNT

DISK - Enum constant in enum class sc.fiji.snt.analysis.ProfileProcessor.Shape

DISK2D - Static variable in class sc.fiji.snt.analysis.PathProfiler

DISK3D - Static variable in class sc.fiji.snt.analysis.PathProfiler

DiskBackedGWDTTracer<T> - Class in sc.fiji.snt.tracing.auto

Disk-backed GWDT tracer for very large images.

DiskBackedGWDTTracer(ImagePlus) - Constructor for class sc.fiji.snt.tracing.auto.DiskBackedGWDTTracer

Creates a new DiskBackedGWDTTracer from an ImagePlus.

DiskBackedGWDTTracer(ImgPlus<T>) - Constructor for class sc.fiji.snt.tracing.auto.DiskBackedGWDTTracer

Creates a new DiskBackedGWDTTracer from an ImgPlus.

DiskBackedGWDTTracer(RandomAccessibleInterval<T>) - Constructor for class sc.fiji.snt.tracing.auto.DiskBackedGWDTTracer

Creates a new DiskBackedGWDTTracer with isotropic spacing (1.0 for each dimension).

DiskBackedGWDTTracer(RandomAccessibleInterval<T>, double[]) - Constructor for class sc.fiji.snt.tracing.auto.DiskBackedGWDTTracer

Creates a new DiskBackedGWDTTracer.

DiskBackedStorageBackend - Class in sc.fiji.snt.tracing.auto.gwdt

Disk-backed storage backend for very large images.

DiskBackedStorageBackend(long[]) - Constructor for class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

DiskBackedStorageBackend(long[], int, int) - Constructor for class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

Creates a disk-backed storage backend with custom cache settings.

DiskCursor3D<T> - Class in sc.fiji.snt.util

Iterate the pixels of an oriented solid disk in 3-space, where the disk is constructed from the unit normal to the circle plane, the center point, and radius.

DiskCursor3D(RandomAccessible<T>, Localizable, long, double[]) - Constructor for class sc.fiji.snt.util.DiskCursor3D

Iterates over a parameterized disk in the target RandomAccessible.

DiskCursor3D(RandomAccessible<T>, Localizable, long, double[], double[]) - Constructor for class sc.fiji.snt.util.DiskCursor3D

Iterates over a parameterized disk in the target RandomAccessible.

dismiss() - Method in class sc.fiji.snt.gui.CostPalette

dismiss() - Method in class sc.fiji.snt.gui.SigmaPalette

dismissed() - Method in interface sc.fiji.snt.gui.CostPalette.Listener

User dismissed without picking.

DISPLAY_PATHS_LINES - Static variable in class sc.fiji.snt.SNT

DISPLAY_PATHS_LINES_AND_DISCS - Static variable in class sc.fiji.snt.SNT

DISPLAY_PATHS_SURFACE - Static variable in class sc.fiji.snt.SNT

displayBanner(String, Color, Component) - Static method in class sc.fiji.snt.gui.GuiUtils

displayCustomPathColors - Variable in class sc.fiji.snt.SNT

displayOnStarting() - Method in class sc.fiji.snt.SNTUI

displayPlot() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd

dispose() - Method in class sc.fiji.snt.analysis.SNTChart

Disposes of this chart and releases its resources.

dispose() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

Clears internal caches and mappings to free memory.

dispose() - Method in class sc.fiji.snt.analysis.TreeStatistics

Clears internal caches and mappings to free memory.

dispose() - Method in class sc.fiji.snt.CurationManager

Unregisters this panel from the monitor.

dispose() - Method in class sc.fiji.snt.gui.MeasureUI

dispose() - Method in class sc.fiji.snt.gui.ScriptRecorder

dispose() - Method in class sc.fiji.snt.gui.SNTCommandFinder

Disposes of this command finder and its associated resources.

dispose() - Method in class sc.fiji.snt.gui.SNTInterpreterPane

dispose() - Method in class sc.fiji.snt.PathAndFillManager

dispose() - Method in class sc.fiji.snt.PathManagerUI

dispose() - Method in class sc.fiji.snt.seed.SeedTableModel

Unregisters the overlay listener and clears the status-cache reference.

dispose() - Method in class sc.fiji.snt.SeedManager

Unregisters the overlay listener and the table-model listener, and closes the detached-table dialog if it's open.

dispose() - Method in class sc.fiji.snt.SNT

dispose() - Method in class sc.fiji.snt.SNTService

Quits SNT.

dispose() - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

dispose() - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

dispose() - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

dispose() - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Clean up resources (close files, free memory, delete temp files).

dispose() - Method in class sc.fiji.snt.viewer.Viewer3D

Closes and releases all the resources used by this viewer.

disposeWithouRecording() - Method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

Closes the dialog without Recording the command.

distance - Variable in class sc.fiji.snt.Fill.Node

distance() - Method in record class sc.fiji.snt.util.TreeUtils.EndpointMatch

Returns the value of the distance record component.

DISTANCE - Enum constant in enum class sc.fiji.snt.FillConverter.ResultType

distanceFromPointToLine(double, double, double, double, double, double, double, double, double) - Static method in class sc.fiji.snt.NearPoint

distanceFromSinglePointPath(double, double, double, double, double, double) - Static method in class sc.fiji.snt.NearPoint

distanceFromSkeleton - Variable in class sc.fiji.snt.analysis.detection.Detection

Distance from the path skeleton at the detection point (physical units)

distanceSqTo(double, double, double) - Method in class sc.fiji.snt.seed.SeedPoint

Squared 3D Euclidean distance to a raw point (physical units).

distanceSqTo(SeedPoint) - Method in class sc.fiji.snt.seed.SeedPoint

Squared 3D Euclidean distance to another seed (physical units).

distanceSquaredTo(double, double, double) - Method in class sc.fiji.snt.util.PointInImage

distanceSquaredTo(PointInImage) - Method in class sc.fiji.snt.util.PointInImage

distanceThreshold - Variable in class sc.fiji.snt.Fill

distanceThreshold(double) - Method in class sc.fiji.snt.analysis.detection.LabelProximityDetector.Config

Sets the maximum distance (in calibrated units) from a label boundary for a node to be considered a contact point.

distanceTo(PointInImage) - Method in class sc.fiji.snt.util.PointInImage

distanceToLineSegment(double, double, double, double, double, double, double, double, double) - Static method in class sc.fiji.snt.NearPoint

distanceToPathNearPoint() - Method in class sc.fiji.snt.NearPoint

Returns the distance to the path, If a corresponding point on the path was found .

distanceToPathPoint() - Method in class sc.fiji.snt.NearPoint

distanceToPathPointSquared() - Method in class sc.fiji.snt.NearPoint

distribution(Supplier<SNTTable>) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

DistributionBPCmd - Class in sc.fiji.snt.gui.cmds

Command for plotting distributions of morphometric properties (branch-related) of Trees

DistributionBPCmd() - Constructor for class sc.fiji.snt.gui.cmds.DistributionBPCmd

DistributionCPCmd - Class in sc.fiji.snt.gui.cmds

Command for plotting distributions of whole-cell morphometric properties of Trees

DistributionCPCmd() - Constructor for class sc.fiji.snt.gui.cmds.DistributionCPCmd

dock() - Method in class sc.fiji.snt.gui.GuiUtils.JTables.DetachableTable

Re-attaches via the caller's redocker.

domain() - Method in record class sc.fiji.snt.analysis.CircularModels.VonMisesFit

Returns the value of the domain record component.

doMorphoFiltering(Collection<Path>, String, Number, Number) - Method in class sc.fiji.snt.gui.PathManagerUISearchableBar

doSearchOnSecondaryData - Variable in class sc.fiji.snt.SNT

DOTCIRCLE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

doublePos - Variable in class sc.fiji.snt.util.CircleCursor3D

doubleSpinner(double, double, double, double, int) - Static method in class sc.fiji.snt.gui.GuiUtils

download(String, File) - Static method in interface sc.fiji.snt.io.RemoteSWCLoader

DOWNLOAD - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

downloadToTempFile(String) - Static method in class sc.fiji.snt.SNTUtils

Downloads a file from the specified URL to a temporary file

downsample(double) - Method in class sc.fiji.snt.Path

Downsamples this path (in-place) by reducing the number of nodes while preserving its overall shape.

downsample(double) - Method in class sc.fiji.snt.Tree

Downsamples the tree, i.e., reduces the density of its nodes by increasing internode spacing.

downsample(ArrayList<SimplePoint>, double) - Static method in class sc.fiji.snt.PathDownsampler

downSample(double) - Method in class sc.fiji.snt.Tree

Deprecated.

Use Tree.downsample(double) instead.

downsampleAll(double) - Method in class sc.fiji.snt.PathAndFillManager

Downsamples alls path using Ramer–Douglas–Peucker simplification.

downsampleToFit(ImgPlus<T>, int) - Static method in class sc.fiji.snt.util.ImgUtils

Downsamples an ImgPlus so that no spatial dimension exceeds maxDimSize.

DRAFT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

draw(Graphics2D, Color) - Method in class sc.fiji.snt.PathNodeCanvas

Draws this node.

drawable - Variable in class sc.fiji.snt.viewer.OBJMesh

drawConnection(Graphics2D, PathNodeCanvas) - Method in class sc.fiji.snt.PathNodeCanvas

drawCrosshairs(Graphics2D, double, double) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

drawDiameter(Graphics2D, int, int) - Method in class sc.fiji.snt.PathNodeCanvas

drawDirectionArrow(Graphics2D, PathNodeCanvas) - Method in class sc.fiji.snt.PathNodeCanvas

Draws a direction arrow pointing from this node toward the next node.

drawDragAndDropPlaceHolder(Component, Graphics2D) - Static method in class sc.fiji.snt.gui.GuiUtils

drawLabel(String, Color) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

Draws a label at the less crowded corner of an ImageJ plot.

drawOverlay(Graphics2D) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

drawOverlay(Graphics2D) - Method in class sc.fiji.snt.MultiPathTracerCanvas

Replaces the parent's PAFM-iterating draw loop with our entry list.

drawOverlay(Graphics2D) - Method in class sc.fiji.snt.TracerCanvas

drawPathAsPoints(Graphics2D, TracerCanvas, SNT) - Method in class sc.fiji.snt.Path

drawPathAsPoints(TracerCanvas, Graphics2D, Color, boolean, boolean, int, int) - Method in class sc.fiji.snt.Path

drawPathAsPoints(TracerCanvas, Graphics2D, Color, int, boolean, boolean) - Method in class sc.fiji.snt.Path

drawPathAsPoints(TracerCanvas, Graphics2D, Color, int, boolean, int, int) - Method in class sc.fiji.snt.Path

drawProgressOnSlice(int, int, TracerCanvas, Graphics) - Method in class sc.fiji.snt.tracing.artist.BiSearchArtist

drawProgressOnSlice(int, int, TracerCanvas, Graphics) - Method in class sc.fiji.snt.tracing.artist.FillerThreadArtist

drawProgressOnSlice(int, int, TracerCanvas, Graphics) - Method in interface sc.fiji.snt.tracing.artist.SearchArtist

drawProgressOnSlice(int, int, TracerCanvas, Graphics) - Method in class sc.fiji.snt.tracing.artist.SearchThreadArtist

dropdownMenuIcon(IconFactory.GLYPH, float, Color) - Static method in class sc.fiji.snt.gui.IconFactory

dropSingletonDimensions(ImgPlus<T>) - Static method in class sc.fiji.snt.util.ImgUtils

Remove singleton dimensions from an ImgPlus, preserving axis metadata.

DrosophilaCompartment - Class in sc.fiji.snt.annotation

Represents a brain region from the Drosophila Anatomy Ontology (FBbt).

DrosophilaCompartment() - Constructor for class sc.fiji.snt.annotation.DrosophilaCompartment

DrosophilaUtils - Class in sc.fiji.snt.annotation

Utility methods for accessing the Drosophila adult brain ontology derived from FBbt (Drosophila Anatomy Ontology).

dump(SNTTable) - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

duplicate() - Method in class sc.fiji.snt.analysis.sholl.Profile

duplicate() - Method in class sc.fiji.snt.viewer.OBJMesh

duplicate() - Method in class sc.fiji.snt.viewer.Viewer3D

Creates a duplicate of this viewer containing only visible objects.

DuplicateCmd - Class in sc.fiji.snt.gui.cmds

GUI command for duplicating a Path.

DuplicateCmd() - Constructor for class sc.fiji.snt.gui.cmds.DuplicateCmd

duration() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.ElongationEvent

Returns the value of the duration record component.

duration() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhase

Returns the value of the duration record component.

duration() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.RetractionEvent

Returns the value of the duration record component.

E

ECCENTRICITY - Static variable in class sc.fiji.snt.analysis.graph.GraphColorMapper

Flag for "Eccentricity" mapping.

ECCENTRICITY_2D - Static variable in class sc.fiji.snt.analysis.ConvexHullAnalyzer

EDGE_WEIGHT - Static variable in class sc.fiji.snt.analysis.graph.GraphColorMapper

Flag for "Edge weight" mapping.

edgeCrossingCostFactor - Variable in class sc.fiji.snt.gui.cmds.mxOrganicLayoutPrefsCmd

Cost factor applied to energy calculations involving edges that cross over one another.

edgeDistanceCostFactor - Variable in class sc.fiji.snt.gui.cmds.mxOrganicLayoutPrefsCmd

Cost factor applied to energy calculations involving the distance nodes and edges.

edgeLengthCostFactor - Variable in class sc.fiji.snt.gui.cmds.mxOrganicLayoutPrefsCmd

Cost factor applied to energy calculations for the edge lengths.

EDGES - Static variable in class sc.fiji.snt.analysis.graph.AnnotationGraph

EDGES - Static variable in class sc.fiji.snt.analysis.graph.GraphColorMapper

edit() - Static method in class sc.fiji.snt.gui.GuiUtils.Buttons

editAt(Component, SeedOverlay, int) - Static method in class sc.fiji.snt.seed.SeedPointEditDialog

Opens a single-seed edit dialog for the seed at the given model-row index of overlay.

editBulk(Component, SeedOverlay, List<Integer>) - Static method in class sc.fiji.snt.seed.SeedPointEditDialog

Opens a bulk edit dialog for all seeds at the given indices.

EDITING - Static variable in class sc.fiji.snt.SNTUI

Flag specifying UI is currently waiting for user to edit a selected Path

editModeAllowed() - Method in class sc.fiji.snt.SNT

Assesses if activation of 'Edit Mode' is possible.

editModeAllowed(boolean) - Method in class sc.fiji.snt.SNT

Checks if edit mode can be enabled.

editModeAllowed(boolean, Path) - Method in class sc.fiji.snt.SNT

Checks if edit mode can be enabled, optionally using a specific path.

eigenvalue - Variable in class sc.fiji.snt.analysis.PCAnalyzer.PrincipalAxis

The eigenvalue associated with this axis

eitherSide - Variable in class sc.fiji.snt.TracerCanvas

ELLIPSIS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

ELLIPSIS_VERTICAL - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

ELONGATION - Static variable in class sc.fiji.snt.analysis.ConvexHullAnalyzer

ElongationEvent(int, int, double, double, double, double, double, double, double) - Constructor for record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.ElongationEvent

Creates an instance of a ElongationEvent record class.

EMPTY_LABEL - Static variable in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

EMPTY_LABEL - Static variable in class sc.fiji.snt.plugin.ShollAnalysisImgCommonCmd

enableAstar(boolean) - Method in class sc.fiji.snt.SNT

Toggles the A* search algorithm (enabled by default)

enableAStarGUI(boolean) - Method in class sc.fiji.snt.SNTUI

Should only be called by SNT.enableAstar(boolean)

enableAutoActivation(boolean) - Method in class sc.fiji.snt.SNT

enableAutoSelectionOfFinishedPath(boolean) - Method in class sc.fiji.snt.SNT

enableComponents(Container, boolean) - Static method in class sc.fiji.snt.gui.GuiUtils

enableEditMode(boolean) - Method in class sc.fiji.snt.SNT

enableLegend(boolean) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

EnableSciViewUpdateSiteCmd - Class in sc.fiji.snt.gui.cmds

Implements the 'EnableSciViewUpdateSite' command.

EnableSciViewUpdateSiteCmd() - Constructor for class sc.fiji.snt.gui.cmds.EnableSciViewUpdateSiteCmd

enableSecondaryLayerTracing(boolean) - Method in class sc.fiji.snt.SNT

enableSnapCursor(boolean) - Method in class sc.fiji.snt.SNT

Enables SNT's XYZ snap cursor feature.

enableSourceVersion(boolean) - Method in class sc.fiji.snt.io.NeuroMorphoLoader

Enables or disables the use of source version URLs.

enableUIupdates - Variable in class sc.fiji.snt.PathAndFillManager

END - Static variable in class sc.fiji.snt.PathNodeCanvas

Flag describing an end point node

end_x_image - Variable in class sc.fiji.snt.tracing.TubularGeodesicsTracer

end_y_image - Variable in class sc.fiji.snt.tracing.TubularGeodesicsTracer

end_z_image - Variable in class sc.fiji.snt.tracing.TubularGeodesicsTracer

ENDED - Enum constant in enum class sc.fiji.snt.FillManagerUI.State

endElement(String, String, String) - Method in class sc.fiji.snt.PathAndFillManager

endFrame() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.ElongationEvent

Returns the value of the endFrame record component.

endFrame() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.RetractionEvent

Returns the value of the endFrame record component.

endIndex() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhase

Returns the value of the endIndex record component.

endLength() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.ElongationEvent

Returns the value of the endLength record component.

endLength() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.RetractionEvent

Returns the value of the endLength record component.

EndpointClusterAnalysis(boolean, PointInImage, double) - Constructor for record class sc.fiji.snt.util.TreeUtils.EndpointClusterAnalysis

Creates an instance of a EndpointClusterAnalysis record class.

EndpointMatch(double, boolean, boolean) - Constructor for record class sc.fiji.snt.util.TreeUtils.EndpointMatch

Creates an instance of a EndpointMatch record class.

endRadius() - Method in class sc.fiji.snt.analysis.sholl.Profile

endTime() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.ElongationEvent

Returns the value of the endTime record component.

endTime() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhase

Returns the value of the endTime record component.

endTime() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.RetractionEvent

Returns the value of the endTime record component.

EnhancedGenericDialog - Class in sc.fiji.snt.gui

Deprecated.

EnhancedGenericDialog(String) - Constructor for class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

GenericDialog constructor

EnhancedGenericDialog(String, Frame) - Constructor for class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

GenericDialog constructor

enhanceTableDisplay(SNTTable, String) - Static method in class sc.fiji.snt.gui.GuiUtils

Enhances a SciJava-managed table display with conveniences (close shortcut, save menu).

enlarge(float) - Method in class sc.fiji.snt.gui.SearchField

enlarge(Roi, int) - Static method in class sc.fiji.snt.analysis.RoiConverter

ensureMaskImgVisibleOnAbort - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

ensureWorkspaceExists() - Method in class sc.fiji.snt.SNTPrefs

Creates workspace directory if it doesn't exist.

entries() - Method in class sc.fiji.snt.analysis.sholl.Profile

Entry(Path, Color, boolean) - Constructor for record class sc.fiji.snt.MultiPathTracerCanvas.Entry

Creates an instance of a Entry record class.

equals(Object) - Method in record class sc.fiji.snt.analysis.CircularModels.VonMisesFit

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class sc.fiji.snt.analysis.curation.CurationTags.Partition

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCalibrator.CheckSummary

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCheck.Warning

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalysisResults.GrowthSummaryStatistics

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.ElongationEvent

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhase

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.RetractionEvent

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.TimePoint

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

equals(Object) - Method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.PolarPeak

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.Report

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in class sc.fiji.snt.analysis.sholl.Profile

equals(Object) - Method in class sc.fiji.snt.annotation.AllenCompartment

equals(Object) - Method in class sc.fiji.snt.annotation.DrosophilaCompartment

equals(Object) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

equals(Object) - Method in record class sc.fiji.snt.io.OmeAxisUtils.OmeMetadata

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class sc.fiji.snt.MultiPathTracerCanvas.Entry

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in class sc.fiji.snt.tracing.BiSearchNode

equals(Object) - Method in class sc.fiji.snt.tracing.DefaultSearchNode

equals(Object) - Method in class sc.fiji.snt.util.BoundingBox

equals(Object) - Method in record class sc.fiji.snt.util.ImgUtils.SliceResult

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in class sc.fiji.snt.util.PointInImage

equals(Object) - Method in class sc.fiji.snt.util.ShollPoint

equals(Object) - Method in class sc.fiji.snt.util.SNTColor

equals(Object) - Method in class sc.fiji.snt.util.SWCPoint

equals(Object) - Method in record class sc.fiji.snt.util.TreeUtils.EndpointClusterAnalysis

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in record class sc.fiji.snt.util.TreeUtils.EndpointMatch

Indicates whether some other object is "equal to" this one.

equals(Object) - Method in class sc.fiji.snt.viewer.Viewer3D

EQUALS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

error(String) - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

error(String) - Method in class sc.fiji.snt.gui.cmds.ComputeSecondaryImg

error(String) - Method in class sc.fiji.snt.gui.cmds.LoadReconstructionCmd

error(String) - Method in class sc.fiji.snt.gui.FileChooser

Displays an error message dialog.

error(String) - Method in class sc.fiji.snt.gui.GuiUtils

error(String) - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

error(String) - Method in class sc.fiji.snt.plugin.BinaryTracerFileCmd

error(String) - Method in class sc.fiji.snt.plugin.GWDTMultiSomaFileCmd

error(String) - Method in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

error(String) - Method in class sc.fiji.snt.plugin.GWDTTracerFileCmd

error(String) - Method in class sc.fiji.snt.plugin.LocalThicknessCmd

error(String) - Method in class sc.fiji.snt.SNT

error(String) - Method in class sc.fiji.snt.SNTUI

error(String) - Static method in class sc.fiji.snt.SNTUtils

error(String, String) - Method in class sc.fiji.snt.gui.GuiUtils

error(String, String, String) - Method in class sc.fiji.snt.gui.GuiUtils

error(String, Throwable) - Static method in class sc.fiji.snt.SNTUtils

ERROR - Enum constant in enum class sc.fiji.snt.analysis.curation.PlausibilityCheck.Severity

Error: the operation is almost certainly wrong.

errorColor() - Static method in class sc.fiji.snt.gui.GuiUtils

errorPrompt(String) - Static method in class sc.fiji.snt.gui.GuiUtils

estimateBackgroundThreshold(RandomAccessibleInterval<? extends RealType<?>>) - Static method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Estimates background threshold using combined range and percentile heuristics.

estimateCostToGoal(int, int, int, boolean) - Method in class sc.fiji.snt.tracing.TracerThread

estimateCostToGoal(int, int, int, int, int, int) - Method in class sc.fiji.snt.tracing.heuristic.Dijkstra

Since Dijkstra's algorithm is equivalent to an A* search where the heuristic function h(x) = 0, return 0.

estimateCostToGoal(int, int, int, int, int, int) - Method in class sc.fiji.snt.tracing.heuristic.Euclidean

estimateCostToGoal(int, int, int, int, int, int) - Method in interface sc.fiji.snt.tracing.heuristic.Heuristic

estimateMemoryUsage() - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

estimateMemoryUsage() - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

estimateMemoryUsage() - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

estimateMemoryUsage() - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Get estimated memory usage in bytes.

estimateMinSomaDistance(List<SomaUtils.SomaResult>) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Estimates the minimum inter-soma distance from a list of detected somas using single-linkage hierarchical clustering with gap analysis.

estimateMinSomaDistance(List<SomaUtils.SomaResult>, RandomAccessibleInterval<T>) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Estimates the minimum inter-soma distance using a hybrid approach: EDT-thickness filtering followed by spatial gap analysis.

estimateWorkingMemoryMB(long[]) - Static method in class sc.fiji.snt.tracing.auto.GWDTTracerFactory

Estimate working memory requirements in MB.

Euclidean - Class in sc.fiji.snt.tracing.heuristic

A* search heuristic using euclidean distance from current node to goal node

Euclidean(Calibration) - Constructor for class sc.fiji.snt.tracing.heuristic.Euclidean

Euclidean(Dataset) - Constructor for class sc.fiji.snt.tracing.heuristic.Euclidean

EUCLIDEAN - Enum constant in enum class sc.fiji.snt.SNT.HeuristicType

euclideanDxTo(PointInImage) - Method in class sc.fiji.snt.util.PointInImage

exceedsDimension(ImgPlus<?>, int) - Static method in class sc.fiji.snt.util.ImgUtils

Checks whether any spatial dimension of an ImgPlus exceeds the given limit.

excludeJunctions(boolean) - Method in class sc.fiji.snt.analysis.detection.AlongPathDetector.Config

Sets AlongPathDetector.Config.excludeJunctions.

execute(Object) - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutGrouped

execute(Object) - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutSorted

exit() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

EXIT_REASONS_STRINGS - Static variable in class sc.fiji.snt.tracing.SearchThread

exitReason - Variable in class sc.fiji.snt.tracing.SearchThread

exitRequested() - Method in class sc.fiji.snt.SNTUI

EXPAND - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

EXPAND_ARROWS1 - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

EXPAND_ARROWS2 - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

expandAllNodes(JTree) - Static method in class sc.fiji.snt.gui.GuiUtils.JTrees

expandNeighbors(BiSearchNode, boolean) - Method in class sc.fiji.snt.tracing.BiSearch

expandNodesOfSameLevel(JTree, TreePath) - Static method in class sc.fiji.snt.gui.GuiUtils.JTrees

expandToLevel(int) - Method in class sc.fiji.snt.gui.OntologyBrowser.OntologyTab

Expands the tree to the given depth level.

expandToLevel(JTree, int) - Static method in class sc.fiji.snt.gui.GuiUtils.JTrees

EXPLORE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

export(String) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphComponent

EXPORT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

exportAllPathsAsSWC(String) - Method in class sc.fiji.snt.PathAndFillManager

Exports all as Paths as SWC file(s).

exportAllPathsAsSWC(Path[], String, String) - Method in class sc.fiji.snt.PathAndFillManager

exportAsCSV(File) - Method in class sc.fiji.snt.analysis.SNTChart

exportConnectedStructureAsSWC(Path, File, String) - Method in class sc.fiji.snt.PathAndFillManager

exportDocument(Document, File) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphComponent

exportFillsAsCSV(File) - Method in class sc.fiji.snt.PathAndFillManager

Export fills as CSV.

exportToCSV(File) - Method in class sc.fiji.snt.PathAndFillManager

Output some potentially useful information about all the Paths managed by this instance as a CSV (comma separated values) file.

exportTree(int, File) - Method in class sc.fiji.snt.PathAndFillManager

extendTips(DirectedWeightedGraph, SWCPoint, double) - Method in class sc.fiji.snt.tracing.auto.ComponentReconnector

Extends leaf tips of the tree across multi-voxel gaps by scanning for bright signal in each leaf's tangent direction and A*-bridging to it.

EXTERNAL_LINK - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

extra - Variable in class sc.fiji.snt.analysis.sholl.ProfileEntry

An ad-hoc measurement associated with this entry's radius

EXTRA - Enum constant in enum class sc.fiji.snt.analysis.sholl.math.ShollStats.DataMode

extractContour(Img<BitType>) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Extracts the boundary contour from a binary mask using Moore boundary tracing.

extractDouble(JTextField) - Static method in class sc.fiji.snt.gui.GuiUtils

extractHemiShellFlag(String) - Static method in class sc.fiji.snt.analysis.sholl.ShollUtils

extractNodes(File, String) - Static method in class sc.fiji.snt.io.MouseLightLoader

Extracts reconstruction(s) from a JSON file.

extractNodes(InputStream, String) - Static method in class sc.fiji.snt.io.MouseLightLoader

extractReadableTimeStamp(File) - Static method in class sc.fiji.snt.SNTUtils

extractTagsFromPath(Path) - Static method in class sc.fiji.snt.PathManagerUI

extractTagsFromPaths(Collection<Path>) - Static method in class sc.fiji.snt.PathManagerUI

extractTrees(File, String) - Static method in class sc.fiji.snt.io.MouseLightLoader

Extracts reconstruction(s) from a JSON file.

extractTrees(InputStream, String) - Static method in class sc.fiji.snt.io.MouseLightLoader

extras() - Method in class sc.fiji.snt.analysis.sholl.Profile

EYE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

EYE_DROPPER - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

EYE_SLASH - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

F

f - Variable in class sc.fiji.snt.tracing.DefaultSearchNode

FALLBACK_CHOICE_KEY - Static variable in class sc.fiji.snt.gui.cmds.PathFitterCmd

FALLBACK_MIN_SEP - Static variable in class sc.fiji.snt.PathFitter

Flag specifying that radii at invalid fit locations should fall back to the minimum voxel separation (voxel size)

FALLBACK_MODE - Static variable in class sc.fiji.snt.PathFitter

Flag specifying that radii at invalid fit locations should fall back to the mode of all possible fits

FALLBACK_NAN - Static variable in class sc.fiji.snt.PathFitter

Flag specifying that radii at invalid fit locations should fall back to Double.NaN

fallbackColor - Variable in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

FAR - Static variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Fast Marching state: voxel has not yet been reached.

farClip - Variable in class sc.fiji.snt.viewer.Bvv.Keyframe

Far clipping distance (slab back).

fCounts - Variable in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

fCounts - Variable in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

FigCreatorCmd - Class in sc.fiji.snt.gui.cmds

SciJava Command for creating publication-ready figures of neuronal reconstructions in 2D and 3D formats with customizable styles and layouts.

FigCreatorCmd() - Constructor for class sc.fiji.snt.gui.cmds.FigCreatorCmd

FILE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

FILE_IMAGE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

fileAvailable(File) - Static method in class sc.fiji.snt.SNTUtils

fileChooser(String, File, int, int) - Static method in class sc.fiji.snt.gui.GuiUtils

FileChooser - Class in sc.fiji.snt.gui

Improvements to JFileChooser, namely:

FileChooser() - Constructor for class sc.fiji.snt.gui.FileChooser

FileDrop - Class in sc.fiji.snt.gui

This class makes it easy to drag and drop files from the operating system to a Java program.

FileDrop(Component, boolean, FileDrop.Listener) - Constructor for class sc.fiji.snt.gui.FileDrop

Constructor with a default border and the option to recursively set drop targets.

FileDrop(Component, Border, boolean, FileDrop.Listener) - Constructor for class sc.fiji.snt.gui.FileDrop

Constructor with a specified border and the option to recursively set drop targets.

FileDrop(Component, Border, FileDrop.Listener) - Constructor for class sc.fiji.snt.gui.FileDrop

Constructor with a specified border

FileDrop(Component, FileDrop.Listener) - Constructor for class sc.fiji.snt.gui.FileDrop

Constructs a FileDrop with a default light-blue border and, if c is a Container, recursively sets all elements contained within as drop targets, though only the top level container will change borders.

FileDrop(PrintStream, Component, boolean, FileDrop.Listener) - Constructor for class sc.fiji.snt.gui.FileDrop

Constructor with a default border, debugging optionally turned on and the option to recursively set drop targets.

FileDrop(PrintStream, Component, Border, boolean, FileDrop.Listener) - Constructor for class sc.fiji.snt.gui.FileDrop

Full constructor with a specified border and debugging optionally turned on.

FileDrop(PrintStream, Component, Border, FileDrop.Listener) - Constructor for class sc.fiji.snt.gui.FileDrop

Constructor with a specified border and debugging optionally turned on.

FileDrop(PrintStream, Component, FileDrop.Listener) - Constructor for class sc.fiji.snt.gui.FileDrop

Constructor with a default border and debugging optionally turned on.

FileDrop.Listener - Interface in sc.fiji.snt.gui

Implement this inner interface to listen for when files are dropped.

FilePicker - Class in sc.fiji.snt.gui

A FilePicker panel similar to Scijava's File widget but adopting SNT's FileChooser.

FilePicker(int, File, String...) - Constructor for class sc.fiji.snt.gui.FilePicker

Default FilePicker constructor.

filesDropped(File[]) - Method in interface sc.fiji.snt.gui.FileDrop.Listener

This method is called when files have been successfully dropped.

Fill - Class in sc.fiji.snt

Defines a filled structure.

Fill() - Constructor for class sc.fiji.snt.Fill

FILL - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

Fill.Node - Class in sc.fiji.snt

Defines a node in a filled structure.

FillConverter - Class in sc.fiji.snt

Map filled nodes from a Collection of FillerThreads to and between RandomAccessibles.

FillConverter(Collection<FillerThread>) - Constructor for class sc.fiji.snt.FillConverter

Constructs a new FillConverter with the specified collection of FillerThread objects.

FillConverter.ResultType - Enum Class in sc.fiji.snt

fillEmptyCells(Object) - Method in class sc.fiji.snt.analysis.SNTTable

Fills all empty cells in the table with the specified value.

FillerProgressCallback - Interface in sc.fiji.snt

The FillerProgressCallback interface extends SearchProgressCallback and provides additional methods specific to monitoring the progress of filler algorithms.

FillerThread - Class in sc.fiji.snt.tracing

Seeded-volume segmentation via single-source shortest paths.

FillerThread(Dataset, double, int, long, Cost) - Constructor for class sc.fiji.snt.tracing.FillerThread

FillerThread(Dataset, double, int, long, Cost, SNT.SearchImageType) - Constructor for class sc.fiji.snt.tracing.FillerThread

FillerThread(Dataset, double, Cost) - Constructor for class sc.fiji.snt.tracing.FillerThread

FillerThread(RandomAccessibleInterval<? extends RealType<?>>, Calibration, double, int, long, Cost) - Constructor for class sc.fiji.snt.tracing.FillerThread

FillerThread(RandomAccessibleInterval<? extends RealType<?>>, Calibration, double, int, long, Cost, SNT.SearchImageType) - Constructor for class sc.fiji.snt.tracing.FillerThread

FillerThread(RandomAccessibleInterval<? extends RealType<?>>, Calibration, double, long, Cost) - Constructor for class sc.fiji.snt.tracing.FillerThread

FillerThread(RandomAccessibleInterval<? extends RealType<?>>, Calibration, double, Cost) - Constructor for class sc.fiji.snt.tracing.FillerThread

FillerThreadArtist - Class in sc.fiji.snt.tracing.artist

An artist class that visualizes the progress and behavior of fill operations performed by filler threads.

FillerThreadArtist(FillerThread, Color, Color) - Constructor for class sc.fiji.snt.tracing.artist.FillerThreadArtist

FILLING_URI - Static variable in class sc.fiji.snt.FillManagerUI

FillManagerUI - Class in sc.fiji.snt

Implements the Fill Manager dialog.

FillManagerUI(SNT) - Constructor for class sc.fiji.snt.FillManagerUI

Instantiates a new Fill Manager Dialog

FillManagerUI.State - Enum Class in sc.fiji.snt

filter(String, double, double) - Method in class sc.fiji.snt.analysis.NodeStatistics

Filters the current pool of nodes matching a measurement-based criterion.

FILTER - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

filterByCableLength(Collection<Tree>, double, double) - Static method in class sc.fiji.snt.util.TreeUtils

Returns the subset of trees whose cable length falls within the specified range.

filterBySize(Collection<Tree>, int, int) - Static method in class sc.fiji.snt.util.TreeUtils

Returns the subset of trees whose path count falls within the specified range.

filtered() - Method in class sc.fiji.snt.seed.SeedOverlay

Returns a new list of seeds whose confidence falls in [lowConfidence, highConfidence].

filterEdges(Predicate<E>) - Method in class sc.fiji.snt.analysis.graph.SNTGraph

Remove edges from this graph that do not match the given predicate.

filterEdgesByWeight(int) - Method in class sc.fiji.snt.analysis.graph.AnnotationGraph

FilterOrTagPathsByAngleCmd - Class in sc.fiji.snt.gui.cmds

Implements PathManagerUI's "Extension Angle(s)" prompt.

FilterOrTagPathsByAngleCmd() - Constructor for class sc.fiji.snt.gui.cmds.FilterOrTagPathsByAngleCmd

filterSomasByIntensity(List<SomaUtils.SomaResult>, RandomAccessibleInterval<T>) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Filters a list of detected somas by sampling the source image intensity at each soma center and applying Otsu's threshold to separate real (bright) somas from false detections (dim).

filterSomasByThickness(List<SomaUtils.SomaResult>, RandomAccessibleInterval<T>) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Filters a list of detected somas by their local EDT thickness, using Otsu's method on the EDT value distribution to separate thick (real soma) from thin (artifact) detections.

filterType - Variable in class sc.fiji.snt.SNT

filterVertices(Predicate<V>) - Method in class sc.fiji.snt.analysis.graph.SNTGraph

Remove vertices from this graph that do not match the given predicate.

find(Collection<Path>, CrossoverFinder.Config) - Static method in class sc.fiji.snt.util.CrossoverFinder

Entry point: detect crossover events for a collection of paths using the given config.

findAllPointsAlongLine(int, int, int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

findBestFit(int, int, double, double) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Computes the 'best fit' polynomial between a specified range of degrees for this profile and keeps the fit in memory.

findBestFit(int, int, PrefService) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Runs LinearProfileStats.findBestFit(int, int, double, double) using the preferences specified by the user using the ShollAnalysisPrefsCmd command.

findClosestEndpoints(Path, Path) - Static method in class sc.fiji.snt.util.TreeUtils

Finds the closest endpoint pairing between two paths.

findClosestPair(File, String) - Static method in class sc.fiji.snt.SNTUtils

findClosestPair(File, String[]) - Static method in class sc.fiji.snt.SNTUtils

findDirectionPeaks(double, double) - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Automatically finds directional peaks (0–360°) over a Sholl radial band by deriving a data-driven prominence threshold (median + 1.5×MAD (Median Absolute Deviation), of local prominences after light smoothing) and applying a minimum separation of two angular bins.

findDirectionPeaks(double, double, int, double) - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Finds up to maxPeaks local maxima in the direction (0–360°) distribution within a Sholl band.

findGraphRoot(DirectedWeightedGraph) - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Finds the root node of a graph.

findJunctionIndices() - Method in class sc.fiji.snt.Path

Returns the indices of nodes which are indicated to be a join, either in this Path object, or any other that starts or ends on it.

findJunctions() - Method in class sc.fiji.snt.Path

Returns the nodes which are indicated to be a join (junction/branch point), either in this Path object, or any other that starts or ends on it.

findMaxima(Path, int) - Method in class sc.fiji.snt.analysis.PathProfiler

Finds the maxima in the profile of the specified path.

findMaxima1D(float[], double) - Static method in class sc.fiji.snt.tracing.CrossSectionUtils

Finds local maxima in a 1D profile using prominence-based filtering.

findMinima(Path, int) - Method in class sc.fiji.snt.analysis.PathProfiler

Finds the minima in the profile of the specified path.

findNode(String) - Method in class sc.fiji.snt.gui.OntologyBrowser.OntologyTab

Finds a node by matching its user object's toString() against the given label (depth-first search).

findOrientationPeaks(double, double) - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Automatically finds orientation (0–180°) peaks over a radial band using the same settings used by PolarProfileStats.findDirectionPeaks(double, double).

findOrientationPeaks(double, double, int, double) - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Finds up to maxPeaks local maxima in the orientation (0–180°) distribution within a Sholl band.

findPathsNeedingReversal(Collection<Path>, PointInImage) - Static method in class sc.fiji.snt.util.TreeUtils

Determines which paths need to be reversed so that their start nodes point toward a given root location.

findPointInStack(int, int, int, int[]) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

findPointInStackPrecise(double, double, int, double[]) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

findRoot(RandomAccessibleInterval<? extends RealType<?>>, double[]) - Static method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Automatically detects the root point using automatic thresholding (Otsu's method).

findRoot(RandomAccessibleInterval<? extends RealType<?>>, double, double[]) - Static method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Automatically detects the most likely root point (soma center) in a neuronal image.

findRootPhysical(RandomAccessibleInterval<? extends RealType<?>>, double[]) - Static method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Automatically detects the root point using automatic thresholding and returns physical coordinates.

findRootPhysical(RandomAccessibleInterval<? extends RealType<?>>, double, double[]) - Static method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Automatically detects the root point and returns physical coordinates.

findSnappingPointInXView(double, double, double[]) - Method in class sc.fiji.snt.SNT

findSpatialAxisIndices(ImgPlus<?>) - Static method in class sc.fiji.snt.util.ImgUtils

Find dimension indices for X, Y, Z axes in an ImgPlus.

findSpatialAxisIndicesWithFallback(ImgPlus<?>) - Static method in class sc.fiji.snt.util.ImgUtils

Find dimension indices for X, Y, Z axes, with fallback to assumed ZYX order.

findThickestPoint(RandomAccessibleInterval<? extends RealType<?>>, double, double[]) - Static method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Finds the thickest point in a foreground structure using the Euclidean Distance Transform (EDT).

findThickestPointPhysical(RandomAccessibleInterval<? extends RealType<?>>, double, double[]) - Static method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Finds the thickest point and converts to physical coordinates.

fineTuningRadius - Variable in class sc.fiji.snt.gui.cmds.mxOrganicLayoutPrefsCmd

The radius below which fine-tuning of the layout should start This involves allowing the distance between nodes and edges to be taken into account in the total energy calculation.

finished(SearchInterface, boolean) - Method in class sc.fiji.snt.FillManagerUI

finished(SearchInterface, boolean) - Method in interface sc.fiji.snt.SearchProgressCallback

finished(SearchInterface, boolean) - Method in class sc.fiji.snt.SNT

finishedPath() - Method in class sc.fiji.snt.SNT

finishOnDoubleConfimation - Variable in class sc.fiji.snt.SNTUI

FIRST_AID - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

firstNode() - Method in class sc.fiji.snt.Path

Returns the first node of this path.

firstRunAfterUpdate() - Static method in class sc.fiji.snt.SNTPrefs

Checks if this is the first run after an SNT update.

FIT_CHOICE_KEY - Static variable in class sc.fiji.snt.gui.cmds.PathFitterCmd

FIT_IN_PLACE_KEY - Static variable in class sc.fiji.snt.gui.cmds.PathFitterCmd

fitFromHistogram(double[], double, CircularModels.Domain) - Static method in class sc.fiji.snt.analysis.CircularModels

Fit von Mises to a weighted histogram over angle bins.

fitFromPairs(double[], double[], CircularModels.Domain) - Static method in class sc.fiji.snt.analysis.CircularModels

Fit von Mises to angle/weight pairs (angles in degrees).

fitPolynomial(int) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Fits sampled data to a polynomial function and keeps the fit in memory.

fitRadii(ImagePlus) - Method in class sc.fiji.snt.Path

Fits radii to this Path by fitting circular cross-sections to the image signal.

fitRadii(ImagePlus) - Method in class sc.fiji.snt.Tree

Fits radii to all paths in this Tree by fitting circular cross-sections to the image signal.

fitted - Variable in class sc.fiji.snt.Path

fittedVersionOf - Variable in class sc.fiji.snt.Path

FITTING_PATHS - Static variable in class sc.fiji.snt.SNTUI

Flag specifying UI is currently waiting for fitting operations to conclude

FIXED - Enum constant in enum class sc.fiji.snt.tracing.auto.AbstractGWDTTracer.WaypointBiasSource

Uniform bias for every waypoint, controlled by AbstractGWDTTracer.setWaypointBiasFixedFactor(double).

flipGraphToHorizontal(boolean) - Method in class sc.fiji.snt.viewer.geditor.TreeGraphComponent

floatingMsg(String, boolean) - Method in class sc.fiji.snt.gui.GuiUtils

floodFillSoma(RandomAccessibleInterval<? extends RealType<?>>, long, long, double) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Creates a binary mask of the soma region using flood fill from seed point.

flush(Collection<SWCPoint>, PrintWriter) - Static method in class sc.fiji.snt.util.SWCPoint

Prints a list of points as space-separated values.

flushSecondaryData() - Method in class sc.fiji.snt.SNT

flushSWCPoints(List<SWCPoint>, PrintWriter, String) - Method in class sc.fiji.snt.PathAndFillManager

FlyCircuitLoader - Class in sc.fiji.snt.io

Absurdly simple importer for retrieving SWC data from FlyCircuit.

FlyCircuitLoader() - Constructor for class sc.fiji.snt.io.FlyCircuitLoader

FOLDER - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

FONT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

FOOTPRINTS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

forceArray(RandomAccessibleInterval<?>, double[]) - Static method in class sc.fiji.snt.tracing.auto.GWDTTracerFactory

Force use of array storage regardless of image size.

forceDisk(RandomAccessibleInterval<?>, double[]) - Static method in class sc.fiji.snt.tracing.auto.GWDTTracerFactory

Force use of disk-backed storage regardless of image size.

forceSparse(RandomAccessibleInterval<?>, double[]) - Static method in class sc.fiji.snt.tracing.auto.GWDTTracerFactory

Force use of sparse storage regardless of image size.

formatButton(AbstractButton, IconFactory.GLYPH) - Method in class sc.fiji.snt.gui.SNTSearchableBar

formatDouble(double, int) - Static method in class sc.fiji.snt.SNTUtils

foundGoal(Path) - Method in class sc.fiji.snt.tracing.SearchThread

foundGoal(Path) - Method in class sc.fiji.snt.tracing.TracerThread

FRACTAL_DIMENSION - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Deprecated.

Use TreeStatistics.BRANCH_FRACTAL_DIMENSION or TreeStatistics.PATH_FRACTAL_DIMENSION instead

fraction() - Method in class sc.fiji.snt.gui.GuiUtils.JTables.VisitingZoom

frame - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

frame - Variable in class sc.fiji.snt.seed.SeedPoint

1-based frame index, or SeedPoint.CT_UNSET.

frame - Variable in class sc.fiji.snt.SNT

frame() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.TimePoint

Returns the value of the frame record component.

frames - Variable in class sc.fiji.snt.viewer.Bvv.Keyframe

Number of frames for the transition from the previous keyframe into this one.

Frangi<T,U> - Class in sc.fiji.snt.filter

A.F.

Frangi(double[], double[], double) - Constructor for class sc.fiji.snt.filter.Frangi

Constructs a Frangi filter with the specified scales, spacing, and stack maximum.

Frangi(double[], double[], double, int) - Constructor for class sc.fiji.snt.filter.Frangi

Constructs a Frangi filter with the specified scales, spacing, stack maximum, and number of threads.

FRANGI - Enum constant in enum class sc.fiji.snt.SNT.FilterType

FREE - Enum constant in enum class sc.fiji.snt.tracing.BiSearchNode.State

FREE - Static variable in class sc.fiji.snt.tracing.SearchThread

freeze() - Method in class sc.fiji.snt.viewer.Viewer3D

Does not allow scene to be interactive.

freezeColumnWidth(JTable, int, int) - Static method in class sc.fiji.snt.gui.GuiUtils.JTables

Auto-sizes the given column to fit its content, then freezes it by setting preferred, minimum, and maximum width to the same value.

fromAWTColor(Color) - Method in class sc.fiji.snt.viewer.Viewer3D

fromBufferedImage(String, BufferedImage) - Static method in class sc.fiji.snt.util.ImpUtils

fromCollection(Collection<Tree>, String) - Static method in class sc.fiji.snt.analysis.TreeStatistics

Creates a TreeStatistics instance from a group of Trees and a specific metric for convenient retrieval of histograms

fromFile(String) - Static method in class sc.fiji.snt.analysis.SNTTable

Script-friendly method for loading CSV data from a file/URL.

fromFile(String) - Static method in class sc.fiji.snt.Tree

Script-friendly method for loading a Tree from a reconstruction file.

fromFile(String, String) - Static method in class sc.fiji.snt.analysis.SNTTable

Script-friendly method for loading tabular data from a file/URL.

fromFileImage() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

fromFill(ImagePlus, ImageStatistics, Fill) - Static method in class sc.fiji.snt.tracing.FillerThread

fromFill(RandomAccessibleInterval<? extends RealType<?>>, Calibration, ImageStatistics, Fill) - Static method in class sc.fiji.snt.tracing.FillerThread

fromGenericTable(GenericTable) - Static method in class sc.fiji.snt.analysis.SNTTable

fromHex(String) - Static method in class sc.fiji.snt.util.SNTColor

Returns an AWT Color from a (#)RRGGBB(AA) hex string.

fromOpenImage() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

fromPaths(List<Path>, RandomAccessibleInterval<? extends RealType<?>>, double[]) - Static method in class sc.fiji.snt.tracing.auto.AutoTraceConfig

Derives auto-trace configuration from one or more example paths.

fromString(String) - Static method in enum class sc.fiji.snt.analysis.sholl.math.ShollStats.DataMode

fromString(String) - Static method in enum class sc.fiji.snt.SNT.CostType

fromString(String) - Static method in class sc.fiji.snt.util.ShollPoint

fromString(String) - Static method in class sc.fiji.snt.util.SNTColor

Returns an AWT Color from any css-valid co

fromString(String) - Static method in class sc.fiji.snt.viewer.Bvv.Keyframe

Deserializes a keyframe from the string produced by Bvv.Keyframe.toString().

fromString(String) - Static method in enum class sc.fiji.snt.viewer.Viewer3D.RotationAxis

FULL_ROTATION - Enum constant in enum class sc.fiji.snt.viewer.Viewer3D.AnimationMode

Continuous 360° rotation (the default).

FUNC_0_GEODESIC - Static variable in class sc.fiji.snt.analysis.PersistenceAnalyzer

The geodesic (i.e., "path") distance from a node to the tree root.

FUNC_1_RADIAL - Static variable in class sc.fiji.snt.analysis.PersistenceAnalyzer

The Euclidean (i.e., "straight line") distance between a node and the tree root.

FUNC_2_CENTRIFUGAL - Static variable in class sc.fiji.snt.analysis.PersistenceAnalyzer

The centrifugal branch order of a node (reverse Strahler number).

FUNC_3_PATH_ORDER - Static variable in class sc.fiji.snt.analysis.PersistenceAnalyzer

The Path order of a node as defined by SNT's path hierarchy.

FUNC_4_X - Static variable in class sc.fiji.snt.analysis.PersistenceAnalyzer

The X coordinate of a node in the spatial coordinate system.

FUNC_5_Y - Static variable in class sc.fiji.snt.analysis.PersistenceAnalyzer

The Y coordinate of a node in the spatial coordinate system.

FUNC_6_Z - Static variable in class sc.fiji.snt.analysis.PersistenceAnalyzer

The Z coordinate of a node in the spatial coordinate system.

FUNC_UNKNOWN - Static variable in class sc.fiji.snt.analysis.PersistenceAnalyzer

fwd() - Method in class sc.fiji.snt.util.CircleCursor3D

fwd() - Method in class sc.fiji.snt.util.DiskCursor3D

fwd() - Method in class sc.fiji.snt.util.PathCursor

G

g - Variable in class sc.fiji.snt.tracing.DefaultSearchNode

GAUGE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

GAUSS - Enum constant in enum class sc.fiji.snt.SNT.FilterType

gaussianCalculated(boolean) - Method in class sc.fiji.snt.SNTUI

geColumnStats(int, int, int) - Method in class sc.fiji.snt.analysis.SNTTable

geColumnStats(String, int, int) - Method in class sc.fiji.snt.analysis.SNTTable

GEM - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

geRowStats(int, int, int) - Method in class sc.fiji.snt.analysis.SNTTable

geRowStats(String, int, int) - Method in class sc.fiji.snt.analysis.SNTTable

geSelectedPathsAsTree() - Method in class sc.fiji.snt.PathManagerUI

Gets the collection of paths listed in the Path Manager as a Tree object.

geSettingsString() - Method in class sc.fiji.snt.SNTUI

get() - Method in class sc.fiji.snt.tracing.image.SupplierUtil.ArraySearchImageSupplier

get() - Method in class sc.fiji.snt.tracing.image.SupplierUtil.ListSearchImageSupplier

get() - Method in class sc.fiji.snt.tracing.image.SupplierUtil.MapSearchImageSupplier

get() - Method in class sc.fiji.snt.util.CircleCursor3D

get() - Method in class sc.fiji.snt.util.PathCursor

get(int) - Method in class sc.fiji.snt.seed.SeedOverlay

get(int) - Method in class sc.fiji.snt.Tree

Returns the Path at the specified position.

get(Container, String) - Static method in class sc.fiji.snt.gui.GuiUtils.Buttons

get(String) - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

Gets the value of a specific convex hull metric.

get(String) - Static method in class sc.fiji.snt.io.NeuroMorphoLoader

Convenience method for retrieving SWC data,

get(String) - Static method in class sc.fiji.snt.util.ColorMaps

Returns a 'core' color table from its title

get(String, String) - Method in class sc.fiji.snt.SNTPrefs

Gets a string preference value.

get(BrainAnnotation) - Method in class sc.fiji.snt.analysis.NodeStatistics

Gets the list of nodes associated with the specified compartment (neuropil label).

get(BrainAnnotation, boolean) - Method in class sc.fiji.snt.analysis.NodeStatistics

Gets the list of nodes associated with the specified compartment (neuropil label).

get(IconFactory.GLYPH, float, Color) - Static method in class sc.fiji.snt.gui.IconFactory

Creates a new icon from a Font Awesome glyph.

get2DBoundingBox(Collection<Path>, int) - Static method in class sc.fiji.snt.analysis.RoiConverter

get2dCentroid(Roi) - Static method in class sc.fiji.snt.analysis.RoiConverter

get3DUniverse() - Method in class sc.fiji.snt.SNT

Deprecated.

get3DViewerResamplingFactor() - Method in class sc.fiji.snt.SNTPrefs

getAbsoluteWindowSize() - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Gets the current absolute window size in frames.

getAcceleratorString() - Method in class sc.fiji.snt.gui.SNTCommandFinder

getAccelName() - Method in class sc.fiji.snt.viewer.Bvv.Keyframe

Returns the current easing type as a human-readable name.

getActiveWindow() - Method in class sc.fiji.snt.SNT

getAdjustedRSquaredOfFit(int) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getAdjustedRSquaredOfFit(int) - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getAliveIndices() - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

getAliveIndices() - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

getAliveIndices() - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

getAliveIndices() - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Returns the set of linear indices that have been marked as ALIVE during Fast Marching.

getAllCompartments() - Static method in class sc.fiji.snt.annotation.DrosophilaUtils

Returns all compartments in the ontology.

getAllFills() - Method in class sc.fiji.snt.PathAndFillManager

getAllIDs() - Static method in class sc.fiji.snt.io.MouseLightQuerier

Gets all available neuron IDs from the database.

getAllLoaders() - Static method in class sc.fiji.snt.io.MouseLightLoader

Gets the loaders for all the cells publicly available in the MouseLight database.

getAllMetrics() - Static method in class sc.fiji.snt.analysis.TreeStatistics

Gets the list of supported metrics.

getAllNeuronIDs() - Static method in class sc.fiji.snt.annotation.InsectBrainUtils

getAllNeuronIDsOrganizedBySpecies() - Static method in class sc.fiji.snt.annotation.InsectBrainUtils

getAllSpecies() - Static method in class sc.fiji.snt.annotation.InsectBrainUtils

getAnalysis() - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

Gets all computed convex hull analysis metrics.

getAnalysis() - Method in class sc.fiji.snt.analysis.RootAngleAnalyzer

getAnalyzer(boolean) - Method in class sc.fiji.snt.SNTService

Deprecated.

Use SNTService.getStatistics(boolean) instead

getAnatomicalPlane(String) - Static method in class sc.fiji.snt.annotation.AllenUtils

Retrieves the anatomical plane matching the specified cartesian plane.

getAncestor(int) - Method in class sc.fiji.snt.annotation.AllenCompartment

Gets the nth ancestor of this compartment.

getAncestor(int) - Method in interface sc.fiji.snt.annotation.BrainAnnotation

Returns the ancestor of this compartment at the specified level.

getAncestor(int) - Method in class sc.fiji.snt.annotation.DrosophilaCompartment

getAncestor(int) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

getAncestors() - Method in class sc.fiji.snt.annotation.AllenCompartment

Gets the ancestor ontologies of this compartment as a flat (non-hierarchical) list.

getAngle(int) - Method in class sc.fiji.snt.Path

Computes the angle between the specified node and its two flanking neighbors.

getAngles() - Method in class sc.fiji.snt.analysis.RootAngleAnalyzer

getAngleStepSize() - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Gets the angular step size in degrees.

getAngleWith(double[]) - Method in class sc.fiji.snt.analysis.PCAnalyzer.PrincipalAxis

Computes the acute angle between this principal axis and a direction vector.

getAngleWith(double, double, double) - Method in class sc.fiji.snt.analysis.PCAnalyzer.PrincipalAxis

Computes the acute angle between this principal axis and a direction vector.

getAngleWithLocalDirection(SNTPoint, double[], String, int) - Method in class sc.fiji.snt.viewer.OBJMesh

Computes the angle between a direction vector and the local mesh direction at a point.

getAngularDistribution() - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Returns the angular distribution obtained by summing the intersections matrix or the length matrix across all radial bins.

getAngularDistribution(double, double) - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Returns the angular distribution obtained by summing only those radial bins whose ring centers fall within the half-open interval [rMin, rMax[.

getAngularDistributionCoherence() - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Convenience getter for PolarProfileStats.Report.adc()

getAnimationAxis() - Method in class sc.fiji.snt.viewer.Viewer3D

Gets the current rotation axis for the live animation.

getAnimationMode() - Method in class sc.fiji.snt.viewer.Viewer3D

Gets the current animation mode.

getAnnotatedFrequencies() - Method in class sc.fiji.snt.analysis.NodeStatistics

Retrieves the count frequencies across brain compartment.

getAnnotatedFrequencies(int) - Method in class sc.fiji.snt.analysis.NodeStatistics

Retrieves the count frequencies across brain compartment.

getAnnotatedFrequencies(int, String) - Method in class sc.fiji.snt.analysis.NodeStatistics

Retrieves the count frequencies across brain compartment.

getAnnotatedFrequenciesByHemisphere(int, Tree) - Method in class sc.fiji.snt.analysis.NodeStatistics

getAnnotatedFrequencyHistogram(int, String, Tree) - Method in class sc.fiji.snt.analysis.NodeStatistics

Retrieves the histogram of count frequencies across brain areas of the specified ontology level across the specified hemisphere.

getAnnotatedHistogram() - Method in class sc.fiji.snt.analysis.NodeStatistics

Retrieves the histogram of count frequencies across brain areas.

getAnnotatedHistogram(int) - Method in class sc.fiji.snt.analysis.NodeStatistics

Retrieves the histogram of count frequencies across brain areas of the specified ontology level.

getAnnotatedLength(int) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getAnnotatedLength(int) - Method in class sc.fiji.snt.analysis.TreeStatistics

Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron.

getAnnotatedLength(int, String) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getAnnotatedLength(int, String) - Method in class sc.fiji.snt.analysis.TreeStatistics

Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron.

getAnnotatedLength(int, String, boolean) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getAnnotatedLength(int, String, boolean) - Method in class sc.fiji.snt.analysis.TreeStatistics

Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron.

getAnnotatedLength(DirectedWeightedGraph, int, char, boolean) - Static method in class sc.fiji.snt.analysis.TreeStatistics

getAnnotatedLengthHistogram() - Method in class sc.fiji.snt.analysis.TreeStatistics

Retrieves the of cable length frequencies across brain areas.

getAnnotatedLengthHistogram(int) - Method in class sc.fiji.snt.analysis.TreeStatistics

Retrieves the histogram of cable length frequencies across brain areas of the specified ontology level.

getAnnotatedLengthHistogram(int, String) - Method in class sc.fiji.snt.analysis.TreeStatistics

Retrieves the histogram of cable length frequencies across brain areas of the specified ontology level across the specified hemisphere.

getAnnotatedLengthHistogram(Map<BrainAnnotation, Double>, int, String) - Method in class sc.fiji.snt.analysis.TreeStatistics

getAnnotatedLengthsByHemisphere(int) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getAnnotatedLengthsByHemisphere(int) - Method in class sc.fiji.snt.analysis.TreeStatistics

Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron in the two brain hemispheres.

getAnnotatedLengthsByHemisphere(DirectedWeightedGraph, int, boolean) - Static method in class sc.fiji.snt.analysis.TreeStatistics

getAnnotatedLengthsByHemisphereHistogram(int) - Method in class sc.fiji.snt.analysis.TreeStatistics

getAnnotatedNodes() - Method in class sc.fiji.snt.analysis.NodeStatistics

Splits the nodes being analyzed into groups sharing the same brain annotation.

getAnnotatedNodes(int) - Method in class sc.fiji.snt.analysis.NodeStatistics

Splits the nodes being analyzed into groups sharing the same brain annotation.

getAnnotation() - Method in class sc.fiji.snt.seed.SeedPoint

getAnnotation() - Method in class sc.fiji.snt.util.PointInImage

getAnnotation() - Method in interface sc.fiji.snt.util.SNTPoint

getAnnotation() - Method in class sc.fiji.snt.util.SWCPoint

getAnnotation(String) - Method in class sc.fiji.snt.viewer.Viewer3D

Gets the annotation associated with the specified label.

getAnnotationGraph() - Method in class sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter

getAnnotations() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getAnnotations() - Method in class sc.fiji.snt.analysis.TreeStatistics

Retrieves the brain compartments (neuropil labels) associated with the Tree being measured innervated by the analyzed neuron.

getAnnotations() - Method in class sc.fiji.snt.io.InsectBrainLoader

Gets the brain compartment annotations for this neuron.

getAnnotations() - Method in class sc.fiji.snt.viewer.Viewer3D

Returns all annotations added to this viewer.

getAnnotations(int) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getAnnotations(int) - Method in class sc.fiji.snt.analysis.TreeStatistics

Retrieves the brain compartments (neuropil labels) associated with the Tree being measured innervated by the analyzed neuron.

getAnnotationsColor() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

getApproximatedSurface() - Method in class sc.fiji.snt.Path

Returns an estimated surface area of this path, treating each inter-node segment as a frustum.

getApproximatedSurface() - Method in class sc.fiji.snt.Tree

Retrieves an approximate estimate of Tree's surface are by approximating the surface area of each path, and summing to total.

getApproximatedVolume() - Method in class sc.fiji.snt.Path

Returns an estimated volume of this path.

getApproximatedVolume() - Method in class sc.fiji.snt.Tree

Retrieves an approximate estimate of Tree's volume by approximating the volume of each path, and summing to total.

getArea() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Returns the soma area in voxels squared.

getAsImage(IconFactory.GLYPH, float, Color) - Static method in class sc.fiji.snt.gui.IconFactory

Creates a new image icon from a Font Awesome glyph.

getAssignedValue() - Method in class sc.fiji.snt.Tree

Retrieves the numeric property assigned to this Tree.

getAutosaveFile() - Method in class sc.fiji.snt.SNTPrefs

getAvailableLuts() - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

Gets the available LUTs.

getAvailableLuts() - Method in class sc.fiji.snt.analysis.NodeColorMapper

Gets the available LUTs.

getAvailableLuts() - Method in class sc.fiji.snt.analysis.TreeColorMapper

Gets the available LUTs.

getAverageElongationRate() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the average rate of elongation events.

getAverageGrowthRate() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the average growth rate (total growth / total time).

getAverageRetractionRate() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the average rate of retraction events.

getAverageSeparation() - Method in class sc.fiji.snt.SNT

getAvgBifurcationRatio() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

getAvgBranchLength() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets average length for all the branches of the analyzed tree.

getAvgContraction() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets average contraction for all the branches of the analyzed tree.

getAvgContractions() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

getAvgExtensionAngle(boolean, int) - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

Gets the average relative extension angle for branches of a specific Strahler order.

getAvgExtensionAngles(boolean) - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

Gets a map of average relative extension angles for all Strahler orders.

getAvgFractalDimension() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the average fractal dimension of the analyzed tree.

getAvgFragmentation() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the average no. of nodes (fragmentation) for all the branches of the analyzed tree.

getAvgFragmentations() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

getAvgPartitionAsymmetry() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the average partition asymmetry of the analyzed tree.

getAvgRemoteBifAngle() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the average remote bifurcation angle of the analyzed tree.

getAxisDefiningSagittalPlane() - Static method in class sc.fiji.snt.annotation.AllenUtils

Gets the axis defining the sagittal plane.

getBackendType() - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

getBackendType() - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

getBackendType() - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

getBackendType() - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Get storage backend type name for logging.

getBackgroundThreshold() - Method in class sc.fiji.snt.tracing.auto.AutoTraceConfig

getBackupCopies(File) - Static method in class sc.fiji.snt.SNTUtils

Returns all timestamped backup copies in the specified location.

getBackupCopies(File, String) - Static method in class sc.fiji.snt.SNTUtils

Returns timestamped backup copies of traces files in the specified location.

getBackupDir() - Method in class sc.fiji.snt.SNTPrefs

Returns the backup directory, or null if workspace doesn't exist.

getBarcode(String) - Method in class sc.fiji.snt.analysis.PersistenceAnalyzer

Gets the persistence barcode for the specified filter function.

getBarycentre() - Method in class sc.fiji.snt.viewer.Annotation3D

Returns the center of this annotation bounding box.

getBaseThresholdFraction() - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Gets the current base threshold fraction for phase classification.

getBatchScriptsMenu() - Method in class sc.fiji.snt.gui.ScriptInstaller

Returns a UI list of SNT's 'Batch' scripts

getBifurcationRatios() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

getBoilerplateScript(String) - Static method in class sc.fiji.snt.gui.ScriptInstaller

getBookmarkManager() - Method in class sc.fiji.snt.SNTUI

Gets the Bookmark Manager pane.

getBoolean(String, boolean) - Method in class sc.fiji.snt.SNTPrefs

Gets a boolean preference value.

getBottomPanel() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

getBoundarySize() - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

Gets the boundary size (perimeter for 2D hulls or surface area for 3D hulls) of the convex hull.

getBoundingBox() - Method in class sc.fiji.snt.Tree

Gets the bounding box associated with this tree.

getBoundingBox(boolean) - Method in class sc.fiji.snt.PathAndFillManager

Returns the BoundingBox enclosing all nodes of all existing Paths.

getBoundingBox(boolean) - Method in class sc.fiji.snt.Tree

Gets the bounding box associated with this tree.

getBoundingBox(String) - Method in class sc.fiji.snt.viewer.OBJMesh

Gets the minimum bounding box of this mesh.

getBoxivity() - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

Gets the boxivity of the convex hull, which measures how box-like the convex hull is.

getBoxPlot(String) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Assembles a Box and Whisker Plot for the specified measurement (cell morphometry).

getBoxPlot(String) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

Assembles a Box and Whisker Plot for the specified measurement (cell morphometry).

getBoxPlot(String) - Method in class sc.fiji.snt.plugin.StrahlerCmd

Returns a boxplot for the specified metric, in which data is grouped by order.

getBoxPlot(String, int, double, boolean) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Assembles a Box and Whisker Plot for the specified feature.

getBoxPlot(String, Collection<BrainAnnotation>) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Assembles a Box and Whisker Plot for the specified feature (absolute measurements).

getBoxPlot(String, Collection<BrainAnnotation>, double, boolean) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Assembles a Box and Whisker Plot for the specified feature.

getBPs() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Gets the branch points (junctions) of the graph.

getBPs() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph

Gets the branch points (junctions) of the graph.

getBPs() - Method in class sc.fiji.snt.Tree

Gets the branch points (junctions) of the graph.

getBrainAreasByStructureId() - Static method in class sc.fiji.snt.annotation.AllenUtils

getBrainAreasByUUID() - Static method in class sc.fiji.snt.annotation.AllenUtils

getBrainAreasList() - Static method in class sc.fiji.snt.annotation.AllenUtils

getBrainAreasList() - Static method in class sc.fiji.snt.annotation.DrosophilaUtils

Returns the list of brain area entries from the bundled JSON.

getBrainCompartments(int, String) - Static method in class sc.fiji.snt.annotation.InsectBrainUtils

getBrainJSON(int) - Static method in class sc.fiji.snt.annotation.InsectBrainUtils

getBrainMeshes(int, String) - Static method in class sc.fiji.snt.annotation.InsectBrainUtils

getBranchCounts() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

getBranches() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getBranches() - Method in class sc.fiji.snt.analysis.PathStatistics

Gets all the paths being analyzed as branches.

getBranches() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

getBranches() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets all the branches in the analyzed tree.

getBranches(int) - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

getBranchingIndex(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Calculates the branching index (BI) as defined in PMID 24503022(doi: 10.1016/j.jneumeth.2014.01.016).

getBranchPoint() - Method in class sc.fiji.snt.Path

Gets the branch point (junction) where this path starts, i.e., connects to its parent path.

getBranchPointCounts() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

getBranchPointDisplay() - Method in class sc.fiji.snt.Path

Returns the branch point as it should be rendered on screen.

getBranchPointIndex() - Method in class sc.fiji.snt.Path

Gets the index of the branch point in the parent path.

getBranchPointMap() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd

getBranchPoints() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getBranchPoints() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the position of all the branch points in the analyzed tree.

getBranchPoints() - Method in class sc.fiji.snt.Path

This is a version of Path.findJunctions() ensuring that a junction node is only retrieved once even if multiple child paths are associated with it.

getBranchPoints(BrainAnnotation) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the position of all the branch points in the analyzed tree associated with the specified annotation.

getBranchPoints(BrainAnnotation, boolean) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the position of all the branch points in the analyzed tree associated with the specified annotation.

getBranchTuneMaxAngle() - Method in class sc.fiji.snt.tracing.auto.AutoTraceConfig

getBreadthFirstIterator() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Gets a BreadthFirstIterator, using the graph root as start vertex.

getBreadthFirstIterator(SWCPoint) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Gets a BreadthFirstIterator, using the specified start vertex.

getButton(float) - Method in class sc.fiji.snt.gui.SNTCommandFinder

getBvvPanel() - Method in class sc.fiji.snt.BookmarkManager

Returns the floating dialog for BVV mode, creating it on first call.

getCableLength() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getCableLength() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the cable length.

getCableLength(BrainAnnotation) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getCableLength(BrainAnnotation) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the cable length associated with the specified compartment (neuropil label).

getCableLength(BrainAnnotation, boolean) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the cable length associated with the specified compartment (neuropil label).

getCableLengthNorm(BrainAnnotation) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the cable length associated with the specified compartment (neuropil label) as a ratio of total length.

getCableLengthNorm(BrainAnnotation, boolean) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the cable length associated with the specified compartment (neuropil label) as a ratio of total length.

getCalibration() - Method in class sc.fiji.snt.io.NeurolucidaImporter

Returns the spatial calibration parsed from the file header.

getCalibration() - Method in class sc.fiji.snt.Path

Gets the spatial calibration of this Path.

getCalibration() - Method in class sc.fiji.snt.SNT

getCalibration() - Method in class sc.fiji.snt.util.BoundingBox

Creates a Calibration object using information from this BoundingBox

getCalibration(ImgPlus<?>) - Static method in class sc.fiji.snt.util.ImgUtils

Extracts ImageJ1 Calibration from ImgPlus axes, including origin offsets.

getCaliperFraction() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Returns the caliper fraction used for limiting Fast Marching spread in multi-soma tracing, or a negative value if the caliper is disabled.

getCanvas(int) - Method in class sc.fiji.snt.SNT

getCanvasLabel() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Returns the string currently rendered on canvas' upper left corner.

getCanvasOffset() - Method in class sc.fiji.snt.Path

Returns the translation offset used to render this Path in a TracerCanvas.

getCartesianPlane(String) - Static method in class sc.fiji.snt.annotation.AllenUtils

Retrieves the Cartesian plane matching the specified anatomical plane.

getCategoryChart() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd

Returns the analysis chart.

getCenter() - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

Returns the center coordinates

getCenteredMaximum() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getCenteredMaximum(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Returns the average coordinates of all maxima.

getCenterFromChoice(String) - Static method in class sc.fiji.snt.plugin.ShollAnalysisTreeCmd

getCenterX() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Returns the center X coordinate in voxels.

getCenterX() - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutGrouped

getCenterY() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Returns the center Y coordinate in voxels.

getCenterY() - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutGrouped

getCenterZ() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Returns the center Z coordinate in voxels, or 0 if 2D.

getCentroid() - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

getCentroid() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getCentroid() - Method in class sc.fiji.snt.util.BoundingBox

getCentroid(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Retrieves the centroid from all pairs of data (radius, inters. counts).

getCentroid(String) - Method in class sc.fiji.snt.viewer.OBJMesh

Returns the spatial centroid of the specified (hemi)mesh.

getCentroids(Collection<Roi>) - Static method in class sc.fiji.snt.analysis.RoiConverter

Extracts centroids from a collection of ROIs as integer pixel coordinates.

getChannel() - Method in class sc.fiji.snt.Path

Gets the hyperstack channel associated with this Path.

getChannel() - Method in class sc.fiji.snt.SNT

getChannel(ImagePlus, int) - Static method in class sc.fiji.snt.util.ImpUtils

getChannelStack(ImagePlus, int) - Static method in class sc.fiji.snt.util.ImpUtils

Returns a lightweight read-only view of a single channel as an ImageStack.

getChart() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd

A variant of PathOrderAnalysisCmd.getCategoryChart() that returns the Analysis chart as a SNTChart object.

getChart() - Method in class sc.fiji.snt.plugin.StrahlerCmd

Returns the 'complete Strahler plot' (e.g., all metrics in a single plot).

getChart() - Method in class sc.fiji.snt.viewer.Viewer2D

Gets the current viewer as a SNTChart object

getChart(String) - Method in class sc.fiji.snt.plugin.StrahlerCmd

Returns a 'Strahler plot' for the specified metric.

getCheckBox() - Method in class sc.fiji.snt.gui.CheckboxSpinner

getCheckedUserObjects(Class<T>) - Method in class sc.fiji.snt.gui.OntologyBrowser

Returns the checked user objects from all tabs, cast to the given type.

getChildren() - Method in class sc.fiji.snt.annotation.AllenCompartment

Gets the child ontologies of this compartment as a flat (non-hierarchical) list.

getChildren() - Method in class sc.fiji.snt.Path

Gets the list of child paths that branch from this path.

getChildren(int) - Method in class sc.fiji.snt.annotation.AllenCompartment

Gets the child ontologies of this compartment as a flat (non-hierarchical) list.

getChoice() - Method in class sc.fiji.snt.gui.DemoRunner

getChoice(String, String, String[], String) - Method in class sc.fiji.snt.gui.GuiUtils

getChoice(String, String, String[], String[], String) - Method in class sc.fiji.snt.gui.GuiUtils

getChoiceAndDouble(String, String, String[], String, Double) - Method in class sc.fiji.snt.gui.GuiUtils

getChoiceWithInput(String, String, String[], String, String) - Method in class sc.fiji.snt.gui.GuiUtils

getChoiceWithOptionAndInfo(String, String, String[], String, String, String, boolean) - Method in class sc.fiji.snt.gui.GuiUtils

Displays a dialog with radio button choices, optional info text, and an optional checkbox.

getChosenTypes(Context) - Static method in class sc.fiji.snt.gui.cmds.SWCTypeFilterCmd

getCircumferencePoints(int, int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

getCol(String) - Method in class sc.fiji.snt.analysis.PathStatistics

getCol(String) - Method in class sc.fiji.snt.analysis.TreeStatistics

getColor() - Method in class sc.fiji.snt.Path

Gets the color of this Path

getColor() - Method in class sc.fiji.snt.Path.PathNode

getColor() - Method in class sc.fiji.snt.Tree

Gets the color assigned to this Tree.

getColor() - Method in class sc.fiji.snt.util.SWCPoint

Gets the color of this point.

getColor() - Method in class sc.fiji.snt.viewer.Annotation3D

getColor(double) - Method in class sc.fiji.snt.analysis.ColorMapper

Gets the color corresponding to the specified mapped value.

getColor(String, Color, String...) - Method in class sc.fiji.snt.gui.GuiUtils

Simplified color chooser.

getColorMap() - Method in class sc.fiji.snt.gui.cmds.SWCTypeOptionsCmd

getColorMode() - Method in class sc.fiji.snt.seed.SeedOverlay

getColorRGB() - Method in class sc.fiji.snt.Path

Gets the color of this Path

getColorRGB(double) - Method in class sc.fiji.snt.analysis.ColorMapper

Gets the color corresponding to the specified mapped value as ColorRGB.

getColorRGB(String, ColorRGB, String...) - Method in class sc.fiji.snt.gui.GuiUtils

Simplified color chooser for ColorRGB.

getColorTable() - Method in class sc.fiji.snt.analysis.ColorMapper

Gets the current color table used for mapping.

getColorTable() - Method in class sc.fiji.snt.analysis.NodeColorMapper

getColorTable() - Method in class sc.fiji.snt.seed.SeedOverlay

getColorTable(String) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

getColorTable(String) - Method in class sc.fiji.snt.analysis.NodeColorMapper

Gets the color table for the specified lookup table name.

getColorTable(String) - Method in class sc.fiji.snt.analysis.TreeColorMapper

getColorTableName() - Method in class sc.fiji.snt.seed.SeedOverlay

getColumnClass(int) - Method in class sc.fiji.snt.seed.SeedTableModel

getColumnCount() - Method in class sc.fiji.snt.seed.SeedTableModel

getColumnHeaders() - Method in class sc.fiji.snt.analysis.SNTTable

getColumnHeaders(String) - Method in class sc.fiji.snt.analysis.SNTTable

getColumnName(int) - Method in class sc.fiji.snt.seed.SeedTableModel

getCompactness() - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

getCompartment(int) - Static method in class sc.fiji.snt.annotation.AllenUtils

Constructs a compartment from its CCF id

getCompartment(int) - Static method in class sc.fiji.snt.annotation.DrosophilaUtils

Returns a DrosophilaCompartment for the given FBbt numeric ID.

getCompartment(String) - Static method in class sc.fiji.snt.annotation.AllenUtils

Constructs a compartment from its CCF name or acronym

getCompartment(String) - Method in class sc.fiji.snt.gui.cmds.MLImporterCmd

Extracts a valid MouseLightLoader compartment flag from input choice

getComponent() - Method in class sc.fiji.snt.gui.SNTInterpreterPane

getComponent() - Method in class sc.fiji.snt.gui.SNTPromptPane

getComponents() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Return the connected components of this graph as a list of new DirectedWeightedGraphs.

getComponentType() - Method in class sc.fiji.snt.gui.SNTInterpreterPane

getComponentType() - Method in class sc.fiji.snt.gui.SNTPromptPane

getConfirmation(String, String) - Method in class sc.fiji.snt.gui.GuiUtils

getConfirmation(String, String) - Method in class sc.fiji.snt.SNT

getConfirmation(String, String, String, String) - Method in class sc.fiji.snt.gui.GuiUtils

getConfirmation2(String, String, String, String) - Method in class sc.fiji.snt.gui.GuiUtils

getConfirmationAndOption(String, String, String, boolean) - Method in class sc.fiji.snt.gui.GuiUtils

getConfirmationAndOption(String, String, String, boolean, String[]) - Method in class sc.fiji.snt.gui.GuiUtils

getConnectedTree(Path) - Static method in class sc.fiji.snt.util.TreeUtils

Gets the connected tree (component) containing the given path.

getConsole() - Static method in class sc.fiji.snt.gui.GuiUtils

getConsole() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

getContext() - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

getContext() - Method in class sc.fiji.snt.SNT

getContext() - Method in class sc.fiji.snt.SNTService

getContext() - Static method in class sc.fiji.snt.SNTUtils

Convenience method to access the context of the running Fiji instance

getContraction() - Method in class sc.fiji.snt.Path

Returns the ratio between the "Euclidean distance" of this path and its length.

getConvexAnalyzer() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the ConvexHullAnalyzer instance associated with this TreeStatistics instance.

getConvexHull() - Method in class sc.fiji.snt.Tree

Retrieves the convex hull defined by all the nodes of this tree.

getConvexHull(String) - Method in class sc.fiji.snt.Tree

Retrieves the convex hull of this tree.

getConvexHullMetric(String) - Method in class sc.fiji.snt.analysis.TreeStatistics

Convenience method to obtain a single-value metric from ConvexHullAnalyzer

getCoordinateOnAxis(int) - Method in class sc.fiji.snt.seed.SeedPoint

getCoordinateOnAxis(int) - Method in class sc.fiji.snt.util.PointInImage

Gets the coordinate along the specified axis.

getCoordinateOnAxis(int) - Method in interface sc.fiji.snt.util.SNTPoint

getCoordinates(String, String, SNTPoint, int) - Method in class sc.fiji.snt.gui.GuiUtils

getCoordinatesInternal(String, String, SNTPoint, String[], int) - Method in class sc.fiji.snt.gui.GuiUtils

getCorrespondences(PathAndFillManager, double) - Method in class sc.fiji.snt.PathAndFillManager

For each point in this PathAndFillManager, find the corresponding point on the other one.

getCostType() - Method in class sc.fiji.snt.SNT

getCount() - Method in class sc.fiji.snt.BookmarkManager

Returns the number of bookmarks.

getCount() - Method in class sc.fiji.snt.viewer.Bvv.AnnotationOverlay

Returns the number of annotations currently in the overlay.

getCountAtRadius(double) - Method in class sc.fiji.snt.analysis.sholl.Profile

getCountMap() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd

getCramerVonMisesStatistic() - Method in class sc.fiji.snt.analysis.RootAngleAnalyzer

Computes the Cramér-von Mises statistic between computed root angles and fitted von Mises distribution.

getCT(ImagePlus, int, int) - Static method in class sc.fiji.snt.util.ImpUtils

getCtSlice(ImagePlus) - Static method in class sc.fiji.snt.util.ImgUtils

getCtSlice(Dataset, int, int) - Static method in class sc.fiji.snt.util.ImgUtils

Get a view of the Dataset at the specified channel and frame.

getCtSlice(ImgPlus<T>) - Static method in class sc.fiji.snt.util.ImgUtils

Extracts a channel/time slice by squeezing singleton dimensions.

getCtSlice(ImgPlus<T>, int, int) - Static method in class sc.fiji.snt.util.ImgUtils

Extract a specific channel/time slice from an ImgPlus.

getCtSlice3d(ImagePlus, int, int) - Static method in class sc.fiji.snt.util.ImgUtils

Get a view of the ImagePlus at the specified channel and frame.

getCtSlice3d(Dataset, int, int) - Static method in class sc.fiji.snt.util.ImgUtils

Get a 3D view of a Dataset at the specified channel and frame.

getCurationManager() - Method in class sc.fiji.snt.SNTUI

Returns the Curation Manager (Curation Assistant).

getCurationsDirectory(File) - Static method in class sc.fiji.snt.analysis.curation.PlausibilityCalibrator

Returns the curations subdirectory inside the given workspace directory.

getCurrentDirectory() - Method in class sc.fiji.snt.gui.FileChooser

getCurrentFile() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

getCurrentImage() - Static method in class sc.fiji.snt.gui.cmds.ChooseDatasetCmd

getCurrentImage() - Static method in class sc.fiji.snt.util.ImpUtils

getCurrentPath() - Method in class sc.fiji.snt.SNT

getCurrentThresholds() - Static method in class sc.fiji.snt.tracing.auto.GWDTTracerFactory

Get current memory thresholds being used.

getCurrentWarnings() - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

getCursorPos() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

getDataMode() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getDataMode() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getDataMode() - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

getDataMode() - Method in interface sc.fiji.snt.analysis.sholl.math.ShollStats

getDataset() - Method in class sc.fiji.snt.SNT

Gets the Image being traced as Dataset.

getDatasetPath(String, int, int) - Static method in class sc.fiji.snt.io.OmeAxisUtils

Get the N5/Zarr dataset path for a given layout and level.

getDateUploaded() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo

getDecimalFormat(double, int) - Static method in class sc.fiji.snt.SNTUtils

getDeepCheck(Class<T>) - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

Convenience method to get a specific deep check by type.

getDeepChecks() - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

getDefaultDirectoryForSaveAs() - Method in class sc.fiji.snt.analysis.SNTChart

getDefaultLookAndFeel() - Static method in class sc.fiji.snt.SNTPrefs

getDefaultName(Path) - Method in class sc.fiji.snt.PathAndFillManager

getDefaultSigma(SNT) - Static method in class sc.fiji.snt.util.SigmaUtils

getDefaultThickness() - Method in class sc.fiji.snt.viewer.Viewer3D

Returns the default line thickness.

getDefaultTransparency() - Method in class sc.fiji.snt.TracerCanvas

getDefColor() - Method in class sc.fiji.snt.viewer.Viewer3D

getDelineationROIs() - Method in class sc.fiji.snt.DelineationsManager

getDelineationsManager() - Method in class sc.fiji.snt.SNTUI

Gets the Delineations Manager pane.

getDensityPlot() - Method in class sc.fiji.snt.analysis.RootAngleAnalyzer

Generates a density plot of the root angles using the fitted von Mises distribution.

getDensityPlot(List<RootAngleAnalyzer>) - Static method in class sc.fiji.snt.analysis.RootAngleAnalyzer

getDepth() - Method in class sc.fiji.snt.analysis.TreeStatistics

Returns the depth of the BoundingBox box of the tree being measured

getDepth() - Method in class sc.fiji.snt.SNT

getDepthFirstIterator() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Gets a DepthFirstIterator, using the graph root as start vertex.

getDepthFirstIterator() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph

getDepthFirstIterator(SWCPoint) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Gets a DepthFirstIterator, using the specified start vertex.

getDepthFirstIterator(SWCPoint) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph

getDescription() - Method in enum class sc.fiji.snt.SNT.CostType

getDescriptiveStatistics() - Method in class sc.fiji.snt.analysis.RootAngleAnalyzer

getDescriptiveStatistics(String) - Method in class sc.fiji.snt.analysis.NodeStatistics

Computes the DescriptiveStatistics for the specified measurement.

getDescriptiveStats(String) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getDescriptiveStats(String) - Method in class sc.fiji.snt.analysis.TreeStatistics

Computes the DescriptiveStatistics for the specified measurement.

getDescriptors() - Static method in class sc.fiji.snt.analysis.PersistenceAnalyzer

Gets a list of supported descriptor functions for persistence analysis.

getDetailedTable() - Method in class sc.fiji.snt.plugin.StrahlerCmd

Gets the detailed table listing individual branch properties aggregated by Strahler order.

getDeterminationRatio() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getDiagonal() - Method in class sc.fiji.snt.util.BoundingBox

Gets the box diagonal

getDiagram(String) - Method in class sc.fiji.snt.analysis.PersistenceAnalyzer

Gets the persistence diagram for the specified filter function.

getDiagramNodes(String) - Method in class sc.fiji.snt.analysis.PersistenceAnalyzer

Gets the tree nodes associated with each point in the persistence diagram.

getDiameter() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Returns the estimated soma diameter in voxels.

getDimensions() - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Gets the image dimensions.

getDimensions() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

getDimensions() - Method in class sc.fiji.snt.util.BoundingBox

Gets this BoundingBox dimensions in real world units.

getDimensions(boolean) - Method in class sc.fiji.snt.util.BoundingBox

Gets this BoundingBox dimensions.

getDisabledComponentColor() - Static method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

Returns the foreground color of disabled components.

getDisabledComponentColor() - Static method in class sc.fiji.snt.gui.GuiUtils

getDisplayedHemisphere() - Method in class sc.fiji.snt.viewer.OBJMesh

Returns the currently displayed hemisphere: "left", "right", or "both".

getDisplayRadii() - Method in class sc.fiji.snt.viewer.Bvv

Returns whether paths are currently rendered with per-node radii as tapered frusta (true) or as simple lines (false).

getDistance(long) - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

getDistance(long) - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

getDistance(long) - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

getDistance(long) - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Get Fast Marching distance at linear index.

getDistanceAtPoint(double, double, double) - Method in class sc.fiji.snt.tracing.FillerThread

getDistinctColors(int) - Static method in class sc.fiji.snt.util.SNTColor

Returns distinct colors based on Kenneth Kelly's 22 colors of maximum contrast (black and white excluded).

getDistinctColors(int, String) - Static method in class sc.fiji.snt.util.SNTColor

Returns distinct colors based on Kenneth Kelly's 22 colors of maximum contrast (black and white excluded).

getDistinctColorsAWT(int) - Static method in class sc.fiji.snt.util.SNTColor

getDistinctColorsHex(int) - Static method in class sc.fiji.snt.util.SNTColor

Returns distinct colors based on Kenneth Kelly's 22 colors of maximum contrast (black and white excluded) as Hex values.

getDistinctColorsHex(int, String) - Static method in class sc.fiji.snt.util.SNTColor

Returns distinct colors based on Kenneth Kelly's 22 colors of maximum contrast (black and white excluded) as Hex values.

getDnDFileChooser() - Static method in class sc.fiji.snt.gui.GuiUtils

getDOI() - Method in class sc.fiji.snt.io.MouseLightLoader

Gets the DOI for this neuron.

getDorsalSign(HashMap<String, String>) - Static method in class sc.fiji.snt.gui.cmds.CustomizeAxesCmd

Returns the sign of the dorsal direction: -1 for negative, +1 for positive.

getDouble(String, String, double, double, double, String) - Method in class sc.fiji.snt.gui.GuiUtils

getDouble(String, String, Number) - Method in class sc.fiji.snt.gui.GuiUtils

getDoublePosition(int) - Method in class sc.fiji.snt.util.CircleCursor3D

getDoublePosition(int) - Method in class sc.fiji.snt.util.PathCursor

getDragInsets() - Method in class sc.fiji.snt.gui.ComponentMover

Get the drag insets

getDrawable() - Method in class sc.fiji.snt.viewer.Annotation3D

Returns the AbstractDrawable associated with this annotation.

getDrawable() - Method in class sc.fiji.snt.viewer.OBJMesh

Returns the DrawableVBO associated with this mesh

getDrawableColor() - Method in class sc.fiji.snt.viewer.Annotation3D

getDrawDiameters() - Method in class sc.fiji.snt.SNT

getDVAxis(HashMap<String, String>) - Static method in class sc.fiji.snt.gui.cmds.CustomizeAxesCmd

Returns the axis identifier ("X", "Y", or "Z") assigned to the Dorsal-Ventral role, or null if none is assigned.

getEccentricity() - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

getEdgeColor(E) - Method in class sc.fiji.snt.analysis.graph.SNTGraph

getEdgeColorRGBMap() - Method in class sc.fiji.snt.analysis.graph.SNTGraph

getEdgeInsets() - Method in class sc.fiji.snt.gui.ComponentMover

Get the bounds insets

getEditableNodeIndex() - Method in class sc.fiji.snt.Path

Gets the position of the node tagged as 'editable', if any.

getEditingNode() - Method in class sc.fiji.snt.SNT

getEditingPath() - Method in class sc.fiji.snt.SNT

getEditor() - Method in class sc.fiji.snt.NotesUI

Returns a reference to the underlying editor pane.

getEditor() - Method in class sc.fiji.snt.viewer.GraphViewer

Gets the GraphEditor for this viewer.

getEffectiveThreshold() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

getEigenvalue() - Method in class sc.fiji.snt.analysis.PCAnalyzer.PrincipalAxis

getEitherSide() - Method in class sc.fiji.snt.TracerCanvas

getElapsedTime(long) - Static method in class sc.fiji.snt.SNTUtils

getElongation() - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

Gets the elongation of the convex hull, which measures how elongated the convex hull is.

getElongationEvents() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the detected elongation events for this neurite.

getElongationFrequency() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalysisResults.GrowthSummaryStatistics

getEnclosingRadius(boolean, double) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Returns the largest radius associated with at least the number of specified counts.

getEnclosingRadius(double) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getEstimatedMeanRadius() - Method in class sc.fiji.snt.Fill

Returns the estimated mean radius of the fill, assuming a cylindric shape

getExitReason() - Method in class sc.fiji.snt.tracing.SearchThread

getExtensionAngle3D(boolean) - Method in class sc.fiji.snt.Path

Returns either the compass bearing or the relative branching angle of this path's 3D extension direction.

getExtensionAngle3D(Vector3d) - Method in class sc.fiji.snt.Path

Returns a single angle representing the 3D extension direction.

getExtensionAngleFromHorizontal() - Method in class sc.fiji.snt.Path

Returns the angle between the path's 3D direction and the horizontal axis.

getExtensionAngleFromVertical() - Method in class sc.fiji.snt.Path

Returns the angle between the path's 3D direction and the vertical axis.

getExtensionAngles(boolean) - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

Gets a map of relative extension angles for all branches in each Strahler order.

getExtensionAngles3D() - Method in class sc.fiji.snt.Path

Returns the complete 3D orientation of this path's extension direction as spherical coordinates using navigation/compass convention.

getExtensionAngleXY() - Method in class sc.fiji.snt.Path

Returns the overall extension angle of this path in the XY plane.

getExtensionAngleXZ() - Method in class sc.fiji.snt.Path

Returns the overall extension angle of this path in the XZ plane.

getExtensionAngleZY() - Method in class sc.fiji.snt.Path

Returns the overall extension angle of this path in the ZY plane.

getExtensionDirection3D() - Method in class sc.fiji.snt.Path

Returns the 3D extension direction vector of this path using linear regression.

getExtraMeasurement() - Method in class sc.fiji.snt.analysis.sholl.Profile

getF(boolean) - Method in class sc.fiji.snt.tracing.BiSearchNode

getFFromGoal() - Method in class sc.fiji.snt.tracing.BiSearchNode

getFFromStart() - Method in class sc.fiji.snt.tracing.BiSearchNode

getFile() - Method in class sc.fiji.snt.gui.FilePicker

getFile() - Method in class sc.fiji.snt.gui.SWCExportDialog

getFile() - Method in class sc.fiji.snt.gui.SWCImportDialog

getFile(File, String) - Method in class sc.fiji.snt.gui.GuiUtils

getFileHeader() - Method in class sc.fiji.snt.gui.SWCExportDialog

getFilePath(ImagePlus) - Static method in class sc.fiji.snt.util.ImpUtils

Returns the file path of an image.

getFill() - Method in class sc.fiji.snt.tracing.FillerThread

getFilledBinaryImp() - Method in class sc.fiji.snt.SNT

getFilledDistanceImp() - Method in class sc.fiji.snt.SNT

getFilledImp() - Method in class sc.fiji.snt.SNT

getFilledLabelImp() - Method in class sc.fiji.snt.SNT

getFillerStack() - Method in class sc.fiji.snt.FillConverter

Merges the input FillerThreads into a single SearchImageStack.

getFillManager() - Method in class sc.fiji.snt.SNTUI

Gets the Fill Manager dialog.

getFillThreshold() - Method in class sc.fiji.snt.SNT

getFillWindowLocation() - Method in class sc.fiji.snt.SNTPrefs

getFilteredImageFile() - Method in class sc.fiji.snt.SNT

Returns the file of the 'secondary image', if any.

getFilterType() - Method in class sc.fiji.snt.SNT

getFinalLength() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the final length of the neurite.

getFinalNodeCosts() - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Returns the per-node cost values after refinement.

getFinalPenalty() - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Returns the total penalty of the path after refinement.

getFitted() - Method in class sc.fiji.snt.Path

Gets the fitted version ('flavor') of this Path.

getFittedRadius(ImagePlus, Roi) - Static method in class sc.fiji.snt.analysis.RoiConverter

Retrieves the radius of a circle with the same area of the specified area ROI.

getFitYValues() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Returns the ordinates of the sampled linear plot of fitted data.

getFitYValues() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getFitYValues() - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

getFitYValues() - Method in interface sc.fiji.snt.analysis.sholl.math.ShollStats

getFitYValues(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getFitYValues(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getFitYValues(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

getFitYValues(boolean) - Method in interface sc.fiji.snt.analysis.sholl.math.ShollStats

getFloatPosition(int) - Method in class sc.fiji.snt.util.CircleCursor3D

getFloatPosition(int) - Method in class sc.fiji.snt.util.PathCursor

getFlowPlot(String, int) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, no cutoff value, and all of the brain regions of the specified ontology depth.

getFlowPlot(String, int) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getFlowPlot(String, int) - Method in class sc.fiji.snt.analysis.TreeStatistics

Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, no cutoff value, and all of the brain regions of the specified ontology depth.

getFlowPlot(String, int, double, boolean) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, no cutoff value, and all of the brain regions of the specified ontology depth

getFlowPlot(String, int, double, boolean) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getFlowPlot(String, int, double, boolean) - Method in class sc.fiji.snt.analysis.TreeStatistics

Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, no cutoff value, and all of the brain regions of the specified ontology depth

getFlowPlot(String, Collection<BrainAnnotation>) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getFlowPlot(String, Collection<BrainAnnotation>) - Method in class sc.fiji.snt.analysis.TreeStatistics

Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, and no cutoff value.

getFlowPlot(String, Collection<BrainAnnotation>, boolean) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, and no cutoff value.

getFlowPlot(String, Collection<BrainAnnotation>, boolean) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getFlowPlot(String, Collection<BrainAnnotation>, boolean) - Method in class sc.fiji.snt.analysis.TreeStatistics

Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, and no cutoff value.

getFlowPlot(String, Collection<BrainAnnotation>, String, double, boolean) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Assembles a Flow plot (aka Sankey diagram) for the specified feature.

getFlowPlot(String, Collection<BrainAnnotation>, String, double, boolean) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getFlowPlot(String, Collection<BrainAnnotation>, String, double, boolean) - Method in class sc.fiji.snt.analysis.TreeStatistics

Assembles a Flow plot (aka Sankey diagram) for the specified feature.

getFollowers() - Method in class sc.fiji.snt.viewer.BvvMultiSource

getForegroundRect(ImagePlus, Number) - Static method in class sc.fiji.snt.util.ImpUtils

Returns the cropping rectangle around non-background values, considering all slices of the stack.

getFractalDimension() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the fractal dimension of each branch in the analyzed tree.

getFractalDimension() - Method in class sc.fiji.snt.Path

Gets the fractal dimension of this path.

getFrame() - Method in class sc.fiji.snt.analysis.SNTChart

getFrame() - Method in class sc.fiji.snt.Path

Gets the hyperstack frame position associated with this Path.

getFrame() - Method in class sc.fiji.snt.SNT

getFrame() - Method in class sc.fiji.snt.viewer.Viewer3D

getFrame(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Gets the frame containing this viewer, optionally controlling its visibility.

getFrame(ImagePlus, int) - Static method in class sc.fiji.snt.util.ImpUtils

getFrameInterval() - Method in class sc.fiji.snt.analysis.growth.GrowthAnalysisResults

Gets the frame interval used in the analysis.

getFullName() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo

getG(boolean) - Method in class sc.fiji.snt.tracing.BiSearchNode

getGFromGoal() - Method in class sc.fiji.snt.tracing.BiSearchNode

getGFromStart() - Method in class sc.fiji.snt.tracing.BiSearchNode

getGraph() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

getGraph() - Method in class sc.fiji.snt.Tree

Assembles a DirectedGraph from this Tree.

getGraph(boolean) - Method in class sc.fiji.snt.Tree

Assembles a DirectedGraph from this Tree.

getGraphComponent() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

getGraphics2D(Graphics) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

getGraphOutline() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

getGraphs() - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Generates a list of DirectedWeightedGraphs from the skeleton image.

getGroup() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

Gets the collection of Trees being analyzed.

getGroups() - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Gets the group identifiers currently queued for analysis.

getGroupStats(String) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Gets the group statistics.

getGrowthPhases() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the detected growth phases for this neurite.

getGWDT(long) - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

getGWDT(long) - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

getGWDT(long) - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

getGWDT(long) - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Get GWDT value at linear index.

getHandle() - Method in class sc.fiji.snt.tracing.DefaultSearchNode

getHeapHandle(boolean) - Method in class sc.fiji.snt.tracing.BiSearchNode

getHeapHandleFromGoal() - Method in class sc.fiji.snt.tracing.BiSearchNode

getHeapHandleFromStart() - Method in class sc.fiji.snt.tracing.BiSearchNode

getHeight() - Method in class sc.fiji.snt.analysis.TreeStatistics

Returns the height of the BoundingBox box of the tree being measured

getHeight() - Method in class sc.fiji.snt.SNT

getHemisphere() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo

getHemisphere() - Method in class sc.fiji.snt.seed.SeedPoint

getHemisphere() - Method in class sc.fiji.snt.util.PointInImage

getHemisphere() - Method in interface sc.fiji.snt.util.SNTPoint

getHemisphere(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils

Checks the hemisphere a neuron belongs to.

getHemisphereFlag(String) - Static method in interface sc.fiji.snt.annotation.BrainAnnotation

getHeuristicType() - Method in class sc.fiji.snt.SNT

getHighConfidence() - Method in class sc.fiji.snt.seed.SeedOverlay

getHighestBranchOrder() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

getHighestOntologyDepth() - Static method in class sc.fiji.snt.annotation.AllenUtils

Gets the maximum number of ontology levels in the Allen CCF.

getHighestPathOrder() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the highest path order of the analyzed tree

getHighestPathOrder() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd

getHistogram(boolean) - Method in class sc.fiji.snt.analysis.RootAngleAnalyzer

Assembles the histogram distribution of root angles.

getHistogram(String) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Gets the relative frequencies histogram for a univariate measurement.

getHistogram(String) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getHistogram(String) - Method in class sc.fiji.snt.analysis.NodeStatistics

Gets the relative frequencies histogram for a univariate measurement.

getHistogram(String) - Method in class sc.fiji.snt.analysis.TreeStatistics

Retrieves the histogram of relative frequencies histogram for a univariate measurement.

getHistogram(String) - Method in class sc.fiji.snt.plugin.StrahlerCmd

Returns a histogram for the specified metric, in which data is grouped by order.

getHistogram(String, AnalysisUtils.HistogramDatasetPlus) - Method in class sc.fiji.snt.analysis.TreeStatistics

getHistogram(List<RootAngleAnalyzer>, boolean) - Static method in class sc.fiji.snt.analysis.RootAngleAnalyzer

getHistogram(SNTTable, boolean) - Static method in class sc.fiji.snt.analysis.SNTChart

getHistogram(SNTTable, int[], boolean) - Static method in class sc.fiji.snt.analysis.SNTChart

Creates a histogram from the given table.

getHistogram(SNTTable, Collection<String>, boolean) - Static method in class sc.fiji.snt.analysis.SNTChart

Creates a histogram from the given table.

getHull() - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

Gets the convex hull object being analyzed.

getID() - Method in class sc.fiji.snt.io.MouseLightLoader

Gets the neuron ID for this loader.

getID() - Method in class sc.fiji.snt.Path

Gets the identifier of this Path

getID() - Method in class sc.fiji.snt.viewer.Viewer3D

Returns this Viewer's id.

getIDs(String, boolean) - Static method in class sc.fiji.snt.io.MouseLightQuerier

Returns a list of IDs associated with the specified identifier

getIDs(Collection<String>, boolean) - Static method in class sc.fiji.snt.io.MouseLightQuerier

Gets neuron IDs matching the specified collection of IDs or DOIs.

getIDs(Collection<AllenCompartment>) - Static method in class sc.fiji.snt.io.MouseLightQuerier

Gets neuron IDs for the specified collection of brain compartments.

getIDs(AllenCompartment) - Static method in class sc.fiji.snt.io.MouseLightQuerier

Gets neuron IDs for the specified brain compartment.

getImage() - Method in class sc.fiji.snt.analysis.SNTChart

Gets an ImagePlus representation of the chart.

getImageFile(File) - Method in class sc.fiji.snt.gui.GuiUtils

getImageFilenamePrefix() - Method in class sc.fiji.snt.SNTUI

getImageIcon(String) - Method in class sc.fiji.snt.gui.SNTSearchableBar

getImagePlus() - Method in class sc.fiji.snt.SNT

Gets the Image being traced.

getImagePlus(int) - Method in class sc.fiji.snt.SNT

Gets the Image associated with a view pane.

getImages(float) - Method in class sc.fiji.snt.analysis.SNTChart

getImgFromImgChoice() - Method in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

getImpContainer(int, int) - Method in class sc.fiji.snt.Tree

Gets an empty image capable of holding the skeletonized version of this tree.

getImpDiagonalLength(boolean, boolean) - Method in class sc.fiji.snt.SNT

getImpInstances() - Static method in class sc.fiji.snt.gui.cmds.ChooseDatasetCmd

getIndex(double[], double) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getIndex(double[], double) - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getIndexOfInters(boolean, double) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Returns the closest index of the intersections data associated with the specified value

getIndexOfRadius(double) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Returns the closest index of sampled distances associated with the specified value

getInitialDirection(int) - Method in class sc.fiji.snt.Path

Returns a (non-normalized) direction vector from the first node to the node at index min(maxNodes, size()-1).

getInitialLength() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the initial length of the neurite.

getInitialNodeCosts() - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Returns the per-node cost values before refinement.

getInitialPenalty() - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Returns the total penalty of the path before refinement.

getInnerBranches() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getInnerBranches() - Method in class sc.fiji.snt.analysis.PathStatistics

Gets the inner branches from the analyzed paths.

getInnerBranches() - Method in class sc.fiji.snt.analysis.TreeStatistics

Retrieves the branches of highest Strahler order in the Tree.

getInnerLength() - Method in class sc.fiji.snt.analysis.PathStatistics

Gets the total length of inner branches.

getInnerLength() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the cable length of inner branches

getInstance() - Method in class sc.fiji.snt.SNTService

Returns a reference to the active SNT instance.

getInstance() - Static method in class sc.fiji.snt.SNTUtils

getInstance() - Static method in class sc.fiji.snt.viewer.Bvv

Returns the most recently created Bvv instance, or null if none has been created yet.

getInt(String, String, int, int, int) - Method in class sc.fiji.snt.gui.GuiUtils

getIntercept() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

Returns the intercept of the estimated regression line,

getInterpolatedPath(double) - Method in class sc.fiji.snt.Path

Returns a new Path in which nodes have been interpolated to ensure that the distance between consecutive nodes does not exceed the specified threshold.

getInterpreter() - Method in class sc.fiji.snt.gui.SNTInterpreterWindow

Returns the underlying ScriptInterpreter for direct evaluation.

getInterpreterPane() - Method in class sc.fiji.snt.gui.SNTInterpreterWindow

getIntersectingRadii() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getIntersectingRadii(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Returns the number of intersecting radii.

getIntPosition(int) - Method in class sc.fiji.snt.util.CircleCursor3D

getIntPosition(int) - Method in class sc.fiji.snt.util.PathCursor

getInvalidTrees() - Method in class sc.fiji.snt.plugin.StrahlerCmd

Returns the Tree(s) that could not be parsed (i.e., topologically invalid)

getIsotropicVoxelSize() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

Gets the isotropic voxel size used for analysis.

getJFreeChart() - Method in class sc.fiji.snt.viewer.Viewer2D

Gets the current viewer as a JFreeChart object

getJSON() - Method in class sc.fiji.snt.io.MouseLightLoader

Gets all the data associated with this reconstruction as a JSON object.

getJTree() - Method in class sc.fiji.snt.PathManagerUI

Gets the JTree component used to display paths.

getJunctionNodes() - Method in class sc.fiji.snt.Path

Deprecated.

use Path.getBranchPoints() instead

getKSTest() - Method in class sc.fiji.snt.analysis.sholl.math.Comparator

Computes the p-value, or observed significance level, of a two-sample Kolmogorov-Smirnov test evaluating the null hypothesis that x and y are samples drawn from the same probability distribution.

getKStestOfFit() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Returns the two-sample Kolmogorov-Smirnov (K-S) test between the polynomial fit and sampled intersections as a measurement of goodness of fit.

getKStestOfFit() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

Returns the two-sample Kolmogorov-Smirnov (K-S) test between the polynomial fit and sampled intersections as a measurement of goodness of fit.

getKurtosis() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getKurtosis(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Calculates the kurtosis.

getLabel() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph

Returns the label identifying this subgraph.

getLabel() - Method in class sc.fiji.snt.Tree

Returns the identifying label of this tree.

getLabel() - Method in class sc.fiji.snt.viewer.Annotation3D

Gets the annotation label

getLabel() - Method in class sc.fiji.snt.viewer.OBJMesh

Deprecated.

use OBJMesh.label instead

getLabels(HashMap<String, String>) - Static method in class sc.fiji.snt.gui.cmds.CustomizeAxesCmd

Returns the axis labels derived from the mapping, suitable for Viewer3D.setAxesLabels().

getLabelsImage(ImagePlus, ColorTable) - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

Gets the labels image.

getLandscape(String, int, int) - Method in class sc.fiji.snt.analysis.PersistenceAnalyzer

Gets the persistence landscape as a vectorized representation.

getLeader() - Method in class sc.fiji.snt.viewer.BvvMultiSource

getLeaderTransform(AffineTransform3D) - Method in class sc.fiji.snt.viewer.BvvMultiSource

Returns a copy of the most recently cached leader fixed transform.

getLength() - Method in class sc.fiji.snt.analysis.graph.AnnotationWeightedEdge

getLength() - Method in class sc.fiji.snt.analysis.graph.SWCWeightedEdge

getLength() - Method in class sc.fiji.snt.Path

Gets the length of this Path

getLengthMap() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd

getLengths() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

getLibraryPane() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

getLinearGrowthRate() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the linear growth rate from regression analysis.

getLinearIntercept() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the y-intercept from linear regression.

getLinearRSquared() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the R-squared value from linear regression.

getLinearStats() - Method in class sc.fiji.snt.analysis.ShollAnalyzer

Gets the LinearProfileStats associated with this analyzer.

getLiveCheck(Class<T>) - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

Convenience method to get a specific live check by type.

getLiveChecks() - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

getLoadedData() - Method in class sc.fiji.snt.SNT

getLoadedDataAsImg(boolean) - Method in class sc.fiji.snt.SNT

getLoadedDataAsImp() - Method in class sc.fiji.snt.SNT

Retrieves the pixel data of the main image currently loaded in memory as an ImagePlus object.

getLoadedFills() - Method in class sc.fiji.snt.PathAndFillManager

getLoadedIterable() - Method in class sc.fiji.snt.SNT

getLocalDirection(SNTPoint, String, int) - Method in class sc.fiji.snt.viewer.OBJMesh

Computes the local direction of the mesh at a specific point using nearest neighbor analysis.

getLongestPath(boolean) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Return the sequence of nodes representing the longest shortest-path in the graph, as a Path.

getLongestPathVertices(boolean) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Return the sequence of nodes representing the longest shortest-path in the graph, as a Deque.

getLongestPhase(GrowthAnalyzer.GrowthPhaseType) - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the longest phase of a specific type.

getLongPosition(int) - Method in class sc.fiji.snt.util.CircleCursor3D

getLongPosition(int) - Method in class sc.fiji.snt.util.PathCursor

getLookAndFeel() - Static method in class sc.fiji.snt.SNTPrefs

Gets the current look and feel preference.

getLowConfidence() - Method in class sc.fiji.snt.seed.SeedOverlay

getLUTs() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

getManagerPanel() - Method in class sc.fiji.snt.viewer.Viewer3D

Returns a reference to control panel.

getMarkerColors() - Method in class sc.fiji.snt.io.NeurolucidaImporter

Returns the colors for each parsed marker, in the same order as NeurolucidaImporter.getMarkerPoints().

getMarkerLabels() - Method in class sc.fiji.snt.io.NeurolucidaImporter

Returns the labels for each parsed marker, in the same order as NeurolucidaImporter.getMarkerPoints().

getMarkerManager() - Method in class sc.fiji.snt.viewer.Bvv

Returns the BookmarkManager used for placing and managing markers in this BVV instance.

getMarkerPoints() - Method in class sc.fiji.snt.io.NeurolucidaImporter

Returns the marker centroids parsed from <marker> elements.

getMask() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

getMaskProcessor(boolean, double[]) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

Creates a 2D 'Sholl heatmap' by applying measured values to the foreground pixels of a copy of the analyzed image.

getMatrix() - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Returns the length matrix with shape [nRadialBins][nAngleBins].

getMax() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getMax(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Returns the largest value of intersection count.

getMaxAngleDeg() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.BranchAngle

getMaxContractionDiff() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.TortuosityConsistency

getMaxDistUm() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.SomaDistance

getMaxEvaluations() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Gets the function evaluation limit for solvers

getMaxGapVoxels() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Returns the maximum number of consecutive dark voxels FM can bridge.

getMaxGWDT() - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

getMaxGWDT() - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

getMaxGWDT() - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

getMaxGWDT() - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Get maximum GWDT value across the entire image.

getMaxHistoryLength() - Method in class sc.fiji.snt.gui.SNTSearchableBar

getMaxima() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getMaxima(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Returns a list of all the points in the linear Sholl profile associated with the highest intersections count

getMaximaRadii() - Method in class sc.fiji.snt.analysis.ShollAnalyzer

getMaxJumpRatio() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.RadiusJumps

getMaxOntologyDepth() - Method in class sc.fiji.snt.analysis.graph.AnnotationGraph

getMaxOrder() - Method in class sc.fiji.snt.plugin.ij1.Strahler

Returns the maximum Strahler order being considered by the plugin.

getMaxOrder(Path) - Static method in class sc.fiji.snt.util.TreeUtils

Returns the maximum path order in the connected tree containing the given path.

getMaxRatio() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.RadiusContinuity

getMaxThickness() - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Gets the maximum thickness for path rendering.

getMean() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getMean(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Calculates the arithmetic mean.

getMeanContraction() - Method in class sc.fiji.snt.tracing.auto.AutoTraceConfig

getMeanIntensity() - Method in class sc.fiji.snt.tracing.auto.AutoTraceConfig

getMeanRadius() - Method in class sc.fiji.snt.Path

Gets the path mean radius.

getMeanRadius() - Method in class sc.fiji.snt.tracing.auto.AutoTraceConfig

getMeanValueOfPolynomialFit(double, double) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Calculates the mean value of polynomial fit using the default integration method (Simpson's).

getMeanValueOfPolynomialFit(String, double, double) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Gets the mean value of polynomial fit.

getMedian() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getMedian(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Calculates the median.

getMenuItem(boolean) - Method in class sc.fiji.snt.gui.SNTCommandFinder

getMesh() - Method in class sc.fiji.snt.analysis.ConvexHull3D

getMesh() - Method in class sc.fiji.snt.annotation.AllenCompartment

getMesh() - Method in interface sc.fiji.snt.annotation.BrainAnnotation

Returns the mesh associated with this compartment.

getMesh() - Method in class sc.fiji.snt.annotation.DrosophilaCompartment

getMesh() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

getMesh(String) - Static method in class sc.fiji.snt.annotation.VFBUtils

Retrieves the mesh associated with the specified VFB id.

getMesh(String) - Method in class sc.fiji.snt.viewer.Viewer3D

Gets the mesh associated with the specified label.

getMesh(String, ColorRGB) - Static method in class sc.fiji.snt.annotation.VFBUtils

Retrieves the mesh associated with the specified VFB id.

getMeshes() - Method in class sc.fiji.snt.io.InsectBrainLoader

Gets the 3D meshes associated with this neuron's brain compartments.

getMeshes() - Method in class sc.fiji.snt.viewer.Viewer3D

Returns all meshes added to this viewer.

getMeshes(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Returns all meshes added to this viewer.

getMeshShadingMode() - Method in class sc.fiji.snt.viewer.Viewer3D

Returns the current mesh shading mode.

getMethod() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getMethodDescription() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getMethodFlag(String) - Static method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getMetric() - Method in class sc.fiji.snt.analysis.graph.AnnotationGraph

getMetric() - Method in class sc.fiji.snt.Fill

getMetric(String) - Method in class sc.fiji.snt.analysis.PathStatistics

Gets a summary metric for the analyzed paths.

getMetric(String) - Method in class sc.fiji.snt.analysis.TreeStatistics

Computes the specified metric.

getMetric(String, Path) - Method in class sc.fiji.snt.analysis.PathStatistics

Gets a specific metric value for an individual path.

getMetricLabel(String, String) - Static method in class sc.fiji.snt.analysis.AnalysisUtils

Assembles a label from a measurements metric and a spatial unit

getMetricLabel(String, Tree) - Static method in class sc.fiji.snt.analysis.AnalysisUtils

Assembles a label from a measurements metric and a spatial unit

getMetrics() - Static method in class sc.fiji.snt.analysis.graph.AnnotationGraph

getMetrics() - Static method in class sc.fiji.snt.analysis.graph.GraphColorMapper

Gets the list of supported mapping metrics.

getMetrics() - Static method in class sc.fiji.snt.analysis.MultiTreeColorMapper

Gets the list of all supported mapping metrics.

getMetrics() - Static method in class sc.fiji.snt.analysis.MultiTreeStatistics

Gets the list of metrics supported by MultiTreeStatistics.

getMetrics() - Static method in class sc.fiji.snt.analysis.NodeColorMapper

Gets the list of supported mapping metrics.

getMetrics() - Static method in class sc.fiji.snt.analysis.NodeStatistics

Gets the list of supported metrics.

getMetrics() - Static method in class sc.fiji.snt.analysis.ProfileProcessor

Gets the array of available ProfileProcessor.Metrics

getMetrics() - Static method in class sc.fiji.snt.analysis.ShollAnalyzer

getMetrics() - Static method in class sc.fiji.snt.analysis.TreeColorMapper

Gets the list of supported mapping metrics.

getMetrics() - Static method in class sc.fiji.snt.analysis.TreeStatistics

Deprecated.

getMetrics(String) - Static method in class sc.fiji.snt.analysis.MultiTreeColorMapper

Gets the list of supported mapping metrics.

getMetrics(String) - Static method in class sc.fiji.snt.analysis.TreeStatistics

Gets a subset of supported metrics.

getMin() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getMin(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Returns the lowest value of intersection count.

getMinAlignmentDeg() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.DirectionContinuity

getMinAngleDeg() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.BranchAngle

getMinBranchIntensityLength() - Method in class sc.fiji.snt.tracing.auto.AutoTraceConfig

getMinContrast() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.SignalQuality

getMinimumSeparation() - Method in class sc.fiji.snt.Path

getMinimumSeparation() - Method in class sc.fiji.snt.SNT

getMinIncreasingRun() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.RadiusMonotonicity

getMinLengthUm() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.TerminalBranchLength

getMinMax() - Method in class sc.fiji.snt.analysis.ColorMapper

Returns the mapping bounds

getMinMax() - Method in class sc.fiji.snt.analysis.NodeColorMapper

getMinMax(ImagePlus) - Static method in class sc.fiji.snt.util.ImpUtils

getMinSomaDistance() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Returns the minimum inter-soma distance (in voxels).

getMinThickness() - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Gets the minimum thickness for path rendering.

getMIP(ImagePlus) - Static method in class sc.fiji.snt.util.ImpUtils

getMIP(ImagePlus, int, int) - Static method in class sc.fiji.snt.util.ImpUtils

getMIP(Collection<ImagePlus>) - Static method in class sc.fiji.snt.util.ImpUtils

getMultipleChoices(String, String[], String) - Method in class sc.fiji.snt.gui.GuiUtils

getMultipleChoicesAndChoice(String, String[], String, boolean, String[], String) - Method in class sc.fiji.snt.gui.GuiUtils

getMultipleTrees() - Method in class sc.fiji.snt.PathManagerUI

getMultiScaleSettings() - Method in class sc.fiji.snt.gui.SigmaPalette

getMultiSources() - Method in class sc.fiji.snt.viewer.Bvv

Returns all BvvMultiSource groups currently managed by this viewer.

getMultiViewer() - Method in class sc.fiji.snt.analysis.MultiTreeColorMapper

getMultiViewer() - Method in class sc.fiji.snt.analysis.TreeColorMapper

Assembles a Multi-pane viewer using all the Trees mapped so far.

getN() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getN() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getN() - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

getN() - Method in interface sc.fiji.snt.analysis.sholl.math.ShollStats

getN(String) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Gets the number of Trees in a specified group.

getName() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.BranchAngle

getName() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.ConstantRadii

getName() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.DeepCheck

getName() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.DirectionContinuity

getName() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.LiveCheck

getName() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.PathOverlap

getName() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.RadiusContinuity

getName() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.RadiusJumps

getName() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.RadiusMonotonicity

getName() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.SignalQuality

getName() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.SomaDistance

getName() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.TerminalBranchLength

getName() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.TortuosityConsistency

getName() - Method in class sc.fiji.snt.Path

Gets this Path's name.

getNaNColor() - Method in class sc.fiji.snt.analysis.ColorMapper

Gets the color used for NaN (Not a Number) values.

getNavigationToolBar() - Method in class sc.fiji.snt.PathManagerUI

getNBranches() - Method in class sc.fiji.snt.analysis.PathStatistics

Gets the number of branches (paths) being analyzed.

getNBranches() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the number of branches in the analyzed tree.

getNBranchPoints(BrainAnnotation) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the number of branch points in the analyzed tree associated with the specified annotation.

getNBranchPoints(BrainAnnotation, boolean) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the number of branch points in the analyzed tree associated with the specified annotation.

getNBranchPointsNorm(BrainAnnotation) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the percentage of branch points in the analyzed tree associated with the specified annotation

getNBranchPointsNorm(BrainAnnotation, boolean) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the percentage of branch points in the analyzed tree associated with the specified annotation

getNetGrowth() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the net growth accounting for retractions.

getNeuriteCount() - Method in class sc.fiji.snt.analysis.growth.GrowthAnalysisResults

Gets the number of analyzed neurites.

getNeuriteGrowthData() - Method in class sc.fiji.snt.analysis.growth.GrowthAnalysisResults

Gets the growth analysis data for all analyzed neurites.

getNeuriteGrowthData(String) - Method in class sc.fiji.snt.analysis.growth.GrowthAnalysisResults

Gets the growth analysis data for a specific neurite.

getNeuriteId() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the unique identifier for this neurite.

getNeuritePhases() - Method in class sc.fiji.snt.analysis.growth.GrowthAnalysisResults

Creates a map of neurite phases suitable for timeline visualization.

getNeuritesByPattern(GrowthAnalysisResults.NeuriteSelectionCriterion) - Method in class sc.fiji.snt.analysis.growth.GrowthAnalysisResults

Gets neurites that show a specific growth pattern or characteristic.

getNeuronCount() - Static method in class sc.fiji.snt.io.MouseLightLoader

Gets the number of cells publicly available in the MouseLight database.

getNeuronCount() - Static method in class sc.fiji.snt.io.MouseLightQuerier

Gets the number of cells publicly available in the MouseLight database.

getNeuronID() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo

getNeuronInfo() - Method in class sc.fiji.snt.io.InsectBrainLoader

getNextImgExtensions() - Method in class sc.fiji.snt.SNTPrefs

Returns the list of filename suffixes used to identify images when navigating to the next/previous image in a folder (see SNTUI).

getNextPoints() - Method in class sc.fiji.snt.util.SWCPoint

Returns the list holding the subsequent nodes in the reconstructed structure after this one.

getNextRow(String) - Method in class sc.fiji.snt.analysis.TreeStatistics

getNFittedPaths() - Method in class sc.fiji.snt.analysis.TreeStatistics

getNNodes() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the number of nodes in the analyzed tree.

getNode() - Method in class sc.fiji.snt.NearPoint

getNode(int) - Method in class sc.fiji.snt.Path

Gets the node at the specified position.

getNode(String) - Method in class sc.fiji.snt.Path

getNodeAnnotation(int) - Method in class sc.fiji.snt.Path

Returns the neuropil annotation associated with this node.

getNodeColor(int) - Method in class sc.fiji.snt.Path

Gets the node color.

getNodeColors() - Method in class sc.fiji.snt.Path

Gets the node colors.

getNodeCount() - Method in class sc.fiji.snt.tracing.auto.AutoTraceConfig

getNodeHemisphereFlag(int) - Method in class sc.fiji.snt.Path

Returns the hemisphere flag associated with this node.

getNodeIndex(PointInImage) - Method in class sc.fiji.snt.Path

Gets the first node index associated with the specified image coordinates.

getNodeList() - Method in class sc.fiji.snt.Fill

Returns the list of nodes in the filled structure.

getNodeRadius(int) - Method in class sc.fiji.snt.Path

Gets the radius of the specified node.

getNodes() - Method in class sc.fiji.snt.analysis.NodeColorMapper

Gets the collection of nodes being mapped.

getNodes() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

getNodes() - Method in class sc.fiji.snt.io.MouseLightLoader

Extracts the nodes (single-point soma, axonal and dendritic arbor) of the loaded neuron.

getNodes() - Method in class sc.fiji.snt.Path

Gets all nodes as a list.

getNodes() - Method in class sc.fiji.snt.Tree

Gets all the nodes (path points) forming this tree.

getNodes(String) - Method in class sc.fiji.snt.io.MouseLightLoader

Script-friendly method to extract the nodes of a cellular compartment.

getNodesAsImage() - Method in class sc.fiji.snt.tracing.BiSearch

getNodesAsImage() - Method in class sc.fiji.snt.tracing.FillerThread

getNodesAsImageFromGoal() - Method in class sc.fiji.snt.tracing.SearchThread

getNodesAsImageFromStart() - Method in class sc.fiji.snt.tracing.SearchThread

getNodesAsSWCPoints() - Method in class sc.fiji.snt.Tree

getNodesByColor() - Method in class sc.fiji.snt.analysis.NodeColorMapper

getNodesCount() - Method in class sc.fiji.snt.Tree

Gets the total number of nodes across all paths in this Tree.

getNodesFromLeavesToRoot() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

getNodesFromRootToLeaves() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

getNodeStatistics() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Gets a NodeStatistics instance for the vertex set

getNodeStatistics() - Method in class sc.fiji.snt.analysis.TreeStatistics

Convenience method to initialize a NodeStatistics from all the nodes of the Tree being analyzed.

getNodeStatistics(String) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Gets a NodeStatistics instance for the nodes in the vertex set of the specified type

getNodeStatistics(String) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph

getNodeStatistics(String) - Method in class sc.fiji.snt.analysis.TreeStatistics

Convenience method to initialize a NodeStatistics from a subset of the nodes of the Tree being analyzed.

getNodeTangent(int) - Method in class sc.fiji.snt.Path

Gets the tangent vector of a specific node.

getNodeUnscaled() - Method in class sc.fiji.snt.NearPoint

getNodeValue(int) - Method in class sc.fiji.snt.Path

Returns the "value" property of this node.

getNodeWithChecks(int) - Method in class sc.fiji.snt.Path

Gets the internal PathNode at the specified position (for advanced operations).

getNodeWithoutChecks(int) - Method in class sc.fiji.snt.Path

Gets the internal PathNode at the specified position (for advanced operations).

getNormalizedMeasurement(String) - Static method in class sc.fiji.snt.analysis.NodeStatistics

getNormalizedMeasurement(String) - Static method in class sc.fiji.snt.analysis.TreeColorMapper

getNormalizedMeasurement(String) - Static method in class sc.fiji.snt.analysis.TreeStatistics

getNormalizer() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getNormalizerDescription() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getNormalizerFlag(String) - Static method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getNormStats() - Method in class sc.fiji.snt.analysis.ShollAnalyzer

Gets the NormalizedProfileStats associated with this analyzer.

getNoSpinesOrVaricosities() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the number of spines/varicosities that have been (manually) assigned to tree being analyzed.

getNotesPane() - Method in class sc.fiji.snt.SNTUI

Gets the Bookmark Manager pane.

getNPaths() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the no. of parsed paths.

getNSomas() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Returns the expected number of somas.

getNTips(BrainAnnotation) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the number of end points in the analyzed tree associated with the specified annotation.

getNTips(BrainAnnotation, boolean) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the number of end points in the analyzed tree associated with the specified annotation.

getNTipsNorm(BrainAnnotation) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the number of end points in the analyzed tree associated with the specified annotation.

getNTipsNorm(BrainAnnotation, boolean) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the percentage of end points in the analyzed tree associated with the specified annotation

getObj() - Method in class sc.fiji.snt.viewer.OBJMesh

Returns the OBJFile associated with this mesh

getOffsets() - Method in class sc.fiji.snt.gui.SWCImportDialog

getOneMinusErfZFudge() - Method in class sc.fiji.snt.SNT

getOntologies() - Static method in class sc.fiji.snt.annotation.AllenUtils

Gets the Allen CCF as a flat (non-hierarchical) collection of ontologies.

getOntologies(int, boolean) - Static method in class sc.fiji.snt.annotation.AllenUtils

Gets a flat (non-hierarchical) list of all the compartments of the specified ontology depth.

getOntologyDepth() - Method in class sc.fiji.snt.annotation.AllenCompartment

Gets the ontology depth of this compartment.

getOntologyDepth() - Method in interface sc.fiji.snt.annotation.BrainAnnotation

Returns the ontology depth of this compartment.

getOntologyDepth() - Method in class sc.fiji.snt.annotation.DrosophilaCompartment

getOntologyDepth() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

getOpenFile(String, File, String...) - Method in class sc.fiji.snt.gui.GuiUtils

getOpenImages() - Static method in class sc.fiji.snt.util.ImpUtils

Returns all currently open images in ImageJ's WindowManager.

getOptions() - Method in class sc.fiji.snt.viewer.Bvv

getOptionsMenu() - Method in class sc.fiji.snt.gui.SearchField

getOrCreateSciViewSNT() - Method in class sc.fiji.snt.SNTService

getOrder() - Method in class sc.fiji.snt.Path

Gets the "bifurcation" (branching) order of this Path.

getOrientationDistributionCoherence() - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Convenience getter for PolarProfileStats.Report.odc()

getOrigin(ImgPlus<?>, AxisType) - Static method in class sc.fiji.snt.util.ImgUtils

Get the origin offset for a specific axis from an ImgPlus.

getOriginalValueOfmxCell(String) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter

getOrigins(ImgPlus<?>) - Static method in class sc.fiji.snt.util.ImgUtils

Get the origin offsets as {xOrigin, yOrigin, zOrigin} from an ImgPlus.

getOrPromptForWorkspace() - Method in class sc.fiji.snt.SNTUI

Returns the workspace directory, prompting user to create it if it doesn't exist.

getOutOfBoundsTransparency() - Method in class sc.fiji.snt.TracerCanvas

getOutput() - Method in class sc.fiji.snt.gui.SNTInterpreterPane

Gets the associated output pane.

getOverlay() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

getPaintScaleLegend(String, ColorTable, double, double, int) - Static method in class sc.fiji.snt.analysis.SNTChart

getPanel() - Method in class sc.fiji.snt.BookmarkManager

getPanel() - Method in class sc.fiji.snt.CurationManager

Builds and returns the panel to be added as a tab in SNTUI.

getPanel() - Method in class sc.fiji.snt.DelineationsManager

getPanel() - Method in class sc.fiji.snt.NotesUI

Returns the assembled Notepad panel.

getParent() - Method in class sc.fiji.snt.annotation.AllenCompartment

Gets the parent of this compartment.

getParent() - Method in interface sc.fiji.snt.annotation.BrainAnnotation

Returns the parent of this compartment.

getParent() - Method in class sc.fiji.snt.annotation.DrosophilaCompartment

getParent() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

getParent() - Method in class sc.fiji.snt.gui.cmds.ComputeSecondaryImg

getParent() - Method in interface sc.fiji.snt.gui.SigmaPaletteListener

getParent(long) - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

getParent(long) - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

getParent(long) - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

getParent(long) - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Get parent pointer at linear index.

getParentPath() - Method in class sc.fiji.snt.Path

Gets the parent path that this path branches from.

getParentStructureId() - Method in class sc.fiji.snt.annotation.AllenCompartment

getParentWindow(JMenuItem) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

getParsedTree() - Method in class sc.fiji.snt.analysis.TreeStatistics

Returns the set of parsed Paths.

getPartitionAsymmetry() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the partition asymmetry at each bifurcation point in the analyzed tree.

getPath() - Method in class sc.fiji.snt.NearPoint

getPath() - Method in class sc.fiji.snt.PathFitter

getPath() - Method in class sc.fiji.snt.util.PointInImage

Returns the Path associated with this node (if any)

getPath(int) - Method in class sc.fiji.snt.PathAndFillManager

Returns the Path at the specified position in the PathAndFillManager list.

getPathAndFillManager() - Method in class sc.fiji.snt.PathManagerUI

Gets the PathAndFillManager instance.

getPathAndFillManager() - Method in class sc.fiji.snt.SNT

getPathAndFillManager() - Method in class sc.fiji.snt.SNTService

Returns the PathAndFillManager associated with the current SNT instance.

getPathCount() - Method in class sc.fiji.snt.tracing.auto.AutoTraceConfig

getPathFrom3DViewerName(String) - Method in class sc.fiji.snt.PathAndFillManager

getPathFromID(int) - Method in class sc.fiji.snt.PathAndFillManager

Returns the Path with the specified id.

getPathFromName(String, boolean) - Method in class sc.fiji.snt.PathAndFillManager

Returns the Path with the specified name.

getPathManager() - Method in class sc.fiji.snt.SNTUI

Gets the Path Manager dialog.

getPaths() - Method in class sc.fiji.snt.gui.PathManagerUISearchableBar

getPaths() - Method in class sc.fiji.snt.PathAndFillManager

Returns the "main" paths managed by this PathAndFillManager.

getPaths() - Method in class sc.fiji.snt.SNTService

Gets the paths currently listed in the Path Manager

getPaths3DDisplay() - Method in class sc.fiji.snt.SNT

Deprecated.

getPathsFiltered() - Method in class sc.fiji.snt.PathAndFillManager

Returns the 'de facto' Paths (excluding null or fitted versions).

getPathsInROI(Roi) - Method in class sc.fiji.snt.PathAndFillManager

getPathsStructured() - Method in class sc.fiji.snt.PathAndFillManager

getPathsStructured(Collection<Path>) - Method in class sc.fiji.snt.PathAndFillManager

getPathWindowLocation() - Method in class sc.fiji.snt.SNTPrefs

getPatternFileFilters() - Method in class sc.fiji.snt.gui.FileChooser

Gets the user 'pattern' file filters (created using the filter by pattern button)

getPercentage(String, String, int) - Method in class sc.fiji.snt.gui.GuiUtils

getPersistentConfirmation(String, String) - Method in class sc.fiji.snt.gui.GuiUtils

getPersistentWarning(String, String) - Method in class sc.fiji.snt.gui.GuiUtils

getPhaseDistribution() - Method in class sc.fiji.snt.analysis.growth.GrowthAnalysisResults

Gets the distribution of growth phase types across all neurites.

getPhaseDistributionForVisualization() - Method in class sc.fiji.snt.analysis.growth.GrowthAnalysisResults

Creates a map suitable for generating phase distribution visualizations.

getPhaseDuration(GrowthAnalyzer.GrowthPhaseType) - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the total duration of phases of a specific type.

getPhasePercentage(GrowthAnalyzer.GrowthPhaseType) - Method in class sc.fiji.snt.analysis.growth.GrowthAnalysisResults

Gets the percentage of phases that are of a specific type.

getPhasePercentage(GrowthAnalyzer.GrowthPhaseType, double) - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the percentage of time spent in a specific phase type.

getPhaseSensitivity() - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Gets the current phase detection sensitivity.

getPixelDepth() - Method in class sc.fiji.snt.SNT

getPixelHeight() - Method in class sc.fiji.snt.SNT

getPixelPositions(boolean) - Method in class sc.fiji.snt.BookmarkManager

Returns a list of points representing the bookmarks.

getPixelWidth() - Method in class sc.fiji.snt.SNT

getPlane() - Method in class sc.fiji.snt.TracerCanvas

Returns the MultiDThreePanes plane associated with this canvas.

getPlausibilityMonitor() - Method in class sc.fiji.snt.SNTUI

Returns the plausibility monitor used by the Curation Manager (Curation Assistant).

getPlot() - Method in class sc.fiji.snt.analysis.PathProfiler

Gets the plot profile as an ImageJ Plot (all channels).

getPlot() - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

getPlot() - Method in class sc.fiji.snt.viewer.Viewer2D

Gets the current plot as a XYPlot object

getPlot(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getPlot(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getPlot(int) - Method in class sc.fiji.snt.analysis.PathProfiler

Gets the plot profile as an ImageJ plot (single-channel).

getPlot(String) - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Returns the polar plot using the specified colormap.

getPlot(ColorTable) - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Returns the polar plot using the specified colormap.

getPlot(Path) - Method in class sc.fiji.snt.analysis.NodeProfiler

getPlot(Path) - Method in class sc.fiji.snt.analysis.PathProfiler

Gets the plot profile as an ImageJ plot (all channels included).

getPlot(Path, int) - Method in class sc.fiji.snt.analysis.NodeProfiler

getPlugin() - Method in class sc.fiji.snt.PathAndFillManager

Gets the SNT instance.

getPlugin() - Method in class sc.fiji.snt.SNTService

Deprecated.

use SNTService.getInstance() instead

getPluginInstance() - Static method in class sc.fiji.snt.SNTUtils

Deprecated.

use SNTUtils.getInstance() instead

getPoint3fList() - Method in class sc.fiji.snt.Path

Deprecated.

getPointDouble(int, double[]) - Method in class sc.fiji.snt.Path

getPointInCanvas(int) - Method in class sc.fiji.snt.Path

getPointInCanvas2D(int, TracerCanvas) - Method in class sc.fiji.snt.Path

getPolarHistogram(String) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Gets the relative frequencies histogram for a univariate measurement as a polar (rose) plot assuming a data range between [0-360].

getPolarHistogram(String) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getPolarHistogram(String) - Method in class sc.fiji.snt.analysis.TreeStatistics

Assembles a polar histogram for the specified metric (assumed to be an angular measurements (e.g., branch angles, path orientations).

getPolygon() - Method in class sc.fiji.snt.analysis.ConvexHull2D

getPolygonCentroid() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getPolygonCentroid(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Calculates the centroid from all (radius, inters. counts) pairs assuming such points define a non-self-intersecting closed polygon.

getPolynomial() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Gets the polynomial function.

getPolynomialAsString(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Returns a string describing the polynomial fit

getPolynomialDegree() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Returns the degree of the polynomial.

getPolynomialMaxima(double, double, double) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Calculates local maxima (critical points at which the derivative of the polynomial is zero) within the specified interval.

getPositions(boolean) - Method in class sc.fiji.snt.BookmarkManager

Returns a list of points representing the bookmarks.

getPredecessor() - Method in class sc.fiji.snt.tracing.DefaultSearchNode

getPredecessorFromGoal() - Method in class sc.fiji.snt.tracing.BiSearchNode

getPredecessorFromStart() - Method in class sc.fiji.snt.tracing.BiSearchNode

getPreferredDirection() - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Convenience getter for PolarProfileStats.Report.pd()

getPreferredDirection(double, double) - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Convenience: preferred direction computed from a radial band [rMin,rMax).

getPreferredOrientation() - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Convenience getter for PolarProfileStats.Report.po()

getPreferredOrientation(double, double) - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Convenience: preferred orientation computed from a radial band [rMin,rMax).

getPreferredSize() - Method in class sc.fiji.snt.viewer.geditor.SNTGraphComponent

getPrefs() - Method in class sc.fiji.snt.SNT

getPrefs() - Method in class sc.fiji.snt.SNTUI

getPreviousEditingPath() - Method in class sc.fiji.snt.SNT

getPrimaryBranches() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getPrimaryBranches() - Method in class sc.fiji.snt.analysis.PathStatistics

Gets the primary branches from the analyzed paths.

getPrimaryBranches() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getPrimaryBranches() - Method in class sc.fiji.snt.analysis.TreeStatistics

Retrieves the primary branches of the analyzed Tree.

getPrimaryBranches(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Returns intersection counts at the smallest radius (inferred no. of primary branches), or the number of the actual number of primary branches specified by LinearProfileStats.setPrimaryBranches(int).

getPrimaryLength() - Method in class sc.fiji.snt.analysis.PathStatistics

Gets the total length of primary branches.

getPrimaryLength() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the cable length of primary branches.

getPrimaryPaths() - Method in class sc.fiji.snt.analysis.TreeStatistics

Retrieves all the Paths in the analyzed Tree tagged as primary.

getPrincipalAxes(String) - Method in class sc.fiji.snt.viewer.OBJMesh

Computes the principal axes of the mesh using Principal Component Analysis (PCA).

getPrincipalAxes(Collection<? extends SNTPoint>) - Static method in class sc.fiji.snt.analysis.PCAnalyzer

Computes the principal axes for a collection of SNTPoints.

getPrincipalAxes(Vertices) - Static method in class sc.fiji.snt.analysis.PCAnalyzer

Computes the principal axes from the vertices of a mesh

getPrincipalAxes(Path) - Static method in class sc.fiji.snt.analysis.PCAnalyzer

Computes the principal axes for a Path structure.

getPrincipalAxes(Tree) - Static method in class sc.fiji.snt.analysis.PCAnalyzer

Computes the principal axes for a Tree structure.

getPrincipalAxes(Tree, boolean) - Static method in class sc.fiji.snt.analysis.PCAnalyzer

Computes the principal axes for a Tree structure with option to exclude root.

getProfile() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getProfile() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getProfile() - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

getProfile() - Method in interface sc.fiji.snt.analysis.sholl.math.ShollStats

getProfile() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

getProfile() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D

getProfile() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser3D

getProfile() - Method in interface sc.fiji.snt.analysis.sholl.parsers.Parser

Gets the Sholl profile generated by the parsing operation.

getProfile() - Method in class sc.fiji.snt.analysis.sholl.parsers.TabularParser

getProfile() - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

getProfile() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCommonCmd

getProfileCopy() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getPrompt() - Method in class sc.fiji.snt.gui.SNTInterpreterPane

Gets the associated prompt pane.

getPromptEditor() - Method in class sc.fiji.snt.gui.SNTInterpreterPane

Gets the associated prompt pane.

getPromptWithCloseHandler(String) - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

Finds the SciJava-generated prompt dialog by its title and attaches a WindowAdapter that resets the UI state to SNTUI.READY when the dialog is closed.

getPromptWithCloseHandler(String, Runnable) - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

Variant of CommonDynamicCmd.getPromptWithCloseHandler(String) that runs an extra action when the dialog is closing (e.g., cleaning up listeners).

getProofReadingToolBar() - Method in class sc.fiji.snt.PathManagerUI

getProperties() - Method in class sc.fiji.snt.analysis.sholl.Profile

getProperties() - Method in class sc.fiji.snt.io.NDFImporter

getProperties() - Method in class sc.fiji.snt.Tree

Returns the Properties instance holding the persistent set of properties.

getProximityUm() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.PathOverlap

getPruneMode() - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Gets the loop pruning strategy.

getR() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

Returns Pearson's product moment correlation coefficient, usually denoted r.

getRadii(double, double, double) - Static method in class sc.fiji.snt.analysis.sholl.ShollUtils

getRadius() - Method in class sc.fiji.snt.Path.PathNode

getRamificationIndex() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getRamificationIndex(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Calculates the ramification index (the highest intersections count divided by the n. of primary branches).

getRange(String, String, float[]) - Method in class sc.fiji.snt.gui.GuiUtils

getRapidThresholdMultiple() - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Gets the current rapid threshold multiple.

getRatioMap() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd

getRawValues(int) - Method in class sc.fiji.snt.analysis.ProfileProcessor

Gets the raw values for each node at the specified step interval.

getRawValues(String) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getReadableVersion() - Static method in class sc.fiji.snt.SNTUtils

getReader(String) - Method in class sc.fiji.snt.io.FlyCircuitLoader

Gets the SWC data associated with the specified cell ID as a reader

getReader(String) - Method in class sc.fiji.snt.io.NeuroMorphoLoader

Gets the SWC data ('CNG version') associated with the specified cell ID as a reader

getReader(String) - Method in interface sc.fiji.snt.io.RemoteSWCLoader

getRealLengthString() - Method in class sc.fiji.snt.Path

getRecentDir() - Method in class sc.fiji.snt.SNTPrefs

getReconnectMaxAngleDeg() - Method in class sc.fiji.snt.tracing.auto.AutoTraceConfig

getReconnectMaxBridgeDist() - Method in class sc.fiji.snt.tracing.auto.AutoTraceConfig

getReconnectMinContraction() - Method in class sc.fiji.snt.tracing.auto.AutoTraceConfig

getReconstructionFile(File, String) - Method in class sc.fiji.snt.gui.GuiUtils

getReconstructionFiles(File) - Method in class sc.fiji.snt.gui.GuiUtils

getReconstructionFiles(File, String) - Static method in class sc.fiji.snt.SNTUtils

Retrieves a list of reconstruction files stored in a common directory matching the specified criteria.

getReconstructionURL(String) - Method in class sc.fiji.snt.io.FlyCircuitLoader

Gets the URL of the SWC file associated with the specified cell ID.

getReconstructionURL(String) - Method in class sc.fiji.snt.io.NeuroMorphoLoader

Gets the URL of the SWC file ('CNG version') associated with the specified cell ID.

getReconstructionURL(String) - Method in interface sc.fiji.snt.io.RemoteSWCLoader

getReconstructionViewer(boolean) - Method in class sc.fiji.snt.SNTUI

Gets the Reconstruction Viewer.

getRecorder(boolean) - Method in class sc.fiji.snt.SNTUI

getRecorder(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Gets the script recorder for this viewer, optionally creating one if needed.

getRecordingCall(AbstractButton) - Static method in class sc.fiji.snt.gui.ScriptRecorder

getRecViewer() - Method in class sc.fiji.snt.SNTService

Returns a reference to the active Reconstruction Viewer (either stand-alone or SNT-associated instance).

getRecViewer(int) - Method in class sc.fiji.snt.SNTService

Returns a reference to an opened Reconstruction Viewer (standalone instance)

getReductionFactor() - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutScaled

getRefBrain() - Static method in class sc.fiji.snt.annotation.ZBAtlasUtils

Retrieves the surface mesh (outline) of the zebrafish template brain.

getRefBrain(String) - Static method in class sc.fiji.snt.annotation.VFBUtils

Retrieves the surface mesh of an adult Drosophila template brain.

getReferenceColor() - Method in class sc.fiji.snt.filter.SpectralSimilarity

Returns the reference color vector used by this filter.

getRegisteredComponent(String) - Method in class sc.fiji.snt.gui.SNTCommandFinder

getRegression() - Method in class sc.fiji.snt.analysis.sholl.math.Comparator

getRegression() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getRelativeExtensionAngle(Path) - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

Computes the relative extension angle for a StrahlerAnalyzer branch by finding the parent direction from the graph structure.

getRemoteBifAngles() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the angle between each bifurcation point and its children in the simplified graph, which comprise either branch points or terminal nodes.

getRenderedTrees() - Method in class sc.fiji.snt.viewer.Bvv

Gets all the trees currently rendered.

getRenderingOptions() - Method in class sc.fiji.snt.viewer.Bvv

Gets the path rendering options for controlling thickness, transparency, etc.

getREPL() - Method in class sc.fiji.snt.gui.SNTInterpreterPane

Gets the associated script REPL.

getReport() - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Returns a cached summary report of the analysis.

getResampledPath(double) - Method in class sc.fiji.snt.Path

Returns a new Path in which nodes have been resampled to ensure uniform spacing along the path.

getResult() - Method in class sc.fiji.snt.tracing.BiSearch

getResult() - Method in class sc.fiji.snt.tracing.FillerThread

getResult() - Method in class sc.fiji.snt.tracing.ManualTracerThread

getResult() - Method in interface sc.fiji.snt.tracing.SearchInterface

getResult() - Method in class sc.fiji.snt.tracing.TracerThread

getResult() - Method in class sc.fiji.snt.tracing.TubularGeodesicsTracer

getResult(Callable<T>) - Static method in class sc.fiji.snt.gui.SwingSafeResult

getRetractionEvents() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the detected retraction events for this neurite.

getRetractionFrequency() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalysisResults.GrowthSummaryStatistics

getRetractionThreshold() - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Gets the current retraction threshold.

getRoi(ImagePlus...) - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

Retrieves the first non-null ROI from the supplied images.

getRois(String, List<double[]>) - Static method in class sc.fiji.snt.BookmarkManager

getRois(String, List<double[]>, Color) - Static method in class sc.fiji.snt.BookmarkManager

Creates a list of PointRois from XYZCT locations with a color tag.

getROIs() - Method in class sc.fiji.snt.analysis.sholl.Profile

getROIs() - Method in class sc.fiji.snt.io.NDFImporter

Converts tracings into ROIs

getROIs(boolean) - Method in class sc.fiji.snt.BookmarkManager

Returns a list of ROIs representing the bookmarks.

getROIs(Overlay, int, int, int) - Static method in class sc.fiji.snt.analysis.RoiConverter

Extracts ROIs associated with a specified CZT position.

getROIs(ImagePlus) - Method in class sc.fiji.snt.analysis.sholl.Profile

getROIs(Path) - Method in class sc.fiji.snt.analysis.RoiConverter

Gets ROI representations of the specified path.

getRoot() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Gets the root of this graph.

getRoot() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph

Gets the root of this graph.

getRoot() - Method in class sc.fiji.snt.Tree

Gets the first node of the main primary path of this tree

getRootAngleAnalyzer() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the RootAngleAnalyzer instance associated with this TreeStatistics instance.

getRootAngleMetric(String) - Method in class sc.fiji.snt.analysis.TreeStatistics

Convenience method to obtain a single-value metric from RootAngleAnalyzer.

getRootAssociatedBranches() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

getRootMesh(ColorRGB) - Static method in class sc.fiji.snt.annotation.AllenUtils

Retrieves the surface contours for the Allen Mouse Brain Atlas (CCF), bundled with SNT.

getRootNumber() - Method in class sc.fiji.snt.analysis.StrahlerAnalyzer

getRootPath(Path) - Static method in class sc.fiji.snt.util.TreeUtils

Gets the root path of the tree containing the given path.

getRootRoiStrategy() - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Gets the current root ROI strategy.

getRootStrategy() - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

Returns the BinaryTracer root strategy constant corresponding to the current BinaryTracerCommonCmd.rootChoice selection.

getRootStrategy() - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Gets the current root strategy.

getRoundness() - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

Gets the roundness of the convex hull, which measures how round or circular the convex hull is.

getRowCount() - Method in class sc.fiji.snt.seed.SeedTableModel

getRSquaredOfFit() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getRSquaredOfFit() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getRSquaredOfFit(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Returns RSquared of the polynomial fit.

getSampleInfo() - Method in class sc.fiji.snt.io.MouseLightLoader

Gets sample information for this neuron.

getSanitizedUnit(String) - Static method in class sc.fiji.snt.SNTUtils

getSaveDir() - Method in class sc.fiji.snt.viewer.geditor.SNTGraphComponent

getSaveFile(String, File, String...) - Method in class sc.fiji.snt.gui.GuiUtils

getScaledPoint() - Method in class sc.fiji.snt.util.PointInCanvas

Converts the pixels coordinates of this point into a physical location if this point is associated with a Path.

getScalingFactors() - Method in class sc.fiji.snt.gui.SWCImportDialog

getSciView() - Method in class sc.fiji.snt.SciViewSNT

Gets the SciView instance currently in use.

getSciViewSNT() - Method in class sc.fiji.snt.SNTService

getSciViewSNT(boolean) - Method in class sc.fiji.snt.SNTUI

Gets the SciViewSNT instance.

getScoreMap() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Returns the current score map, whether externally provided or internally computed.

getScoreMapScales() - Method in class sc.fiji.snt.tracing.auto.AutoTraceConfig

getScriptsDir() - Method in class sc.fiji.snt.gui.ScriptInstaller

getScriptsMenu() - Method in class sc.fiji.snt.gui.ScriptInstaller

Returns a UI list with all the bundled non-demo SNT scripts

getScriptsMenu(Pattern, String...) - Method in class sc.fiji.snt.gui.ScriptInstaller

Returns a UI list with the bundled SNT scripts (specified directories only).

getScrollPane() - Method in class sc.fiji.snt.gui.SNTEditorPane

Gets the scroll pane containing this editor.

getScrollPane() - Method in class sc.fiji.snt.gui.SNTPromptPane

Returns the RTextScrollPane wrapping this prompt.

getSearch() - Method in class sc.fiji.snt.tracing.artist.BiSearchArtist

getSearch() - Method in class sc.fiji.snt.tracing.artist.FillerThreadArtist

getSearch() - Method in interface sc.fiji.snt.tracing.artist.SearchArtist

getSearch() - Method in class sc.fiji.snt.tracing.artist.SearchThreadArtist

getSearchable() - Method in class sc.fiji.snt.PathManagerUI

Gets the Searchable interface for the JTree.

getSearchableBar() - Method in class sc.fiji.snt.gui.OntologyBrowser.OntologyTab

Returns the search bar for additional configuration.

getSearchField() - Method in class sc.fiji.snt.gui.SNTSearchableBar

getSearchImageType() - Method in class sc.fiji.snt.SNT

getSearchType() - Method in class sc.fiji.snt.SNT

getSecondaryData() - Method in class sc.fiji.snt.SNT

getSecondaryDataAsImp() - Method in class sc.fiji.snt.SNT

Retrieves the 'secondary image' data currently loaded in memory as an ImagePlus object.

getSecondaryImageMinMax() - Method in class sc.fiji.snt.SNT

getSecondaryMaxima() - Method in class sc.fiji.snt.analysis.ShollAnalyzer

getSection(int, int) - Method in class sc.fiji.snt.Path

Gets a section between two nodes of this Path.

getSeedOverlay() - Method in class sc.fiji.snt.SNT

Returns the SeedOverlay associated with this SNT instance.

getSelectedColor() - Method in class sc.fiji.snt.gui.ColorChooserButton

getSelectedLeaves() - Method in class sc.fiji.snt.gui.OntologyBrowser

Returns only the leaf-level names of checked selections (without ancestor prefixes).

getSelectedPaths() - Method in class sc.fiji.snt.gui.OntologyBrowser

Returns the checked selections from all tabs as "::"- delimited hierarchical paths.

getSelectedPaths() - Method in class sc.fiji.snt.PathAndFillManager

Gets all paths selected in the GUI

getSelectedPaths() - Method in class sc.fiji.snt.SNT

getSelectedPaths() - Method in class sc.fiji.snt.SNTService

Gets the paths currently selected in the Path Manager list.

getSelectedPaths(boolean) - Method in class sc.fiji.snt.PathManagerUI

Gets the paths currently selected in the Manager's JTree list.

getSelectedPathsOrganizedByTrees(boolean) - Method in class sc.fiji.snt.PathManagerUI

Gets the paths currently selected in the Manager's JTree list as Trees.

getSelectedSeeds() - Method in class sc.fiji.snt.seed.SeedOverlay

getSelectedSWCColor() - Method in class sc.fiji.snt.gui.ColorMenu

getSelectionColor() - Static method in class sc.fiji.snt.gui.GuiUtils

getSessionsDir() - Method in class sc.fiji.snt.SNTPrefs

Returns the sessions directory, or null if workspace doesn't exist.

getSex() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo

getShapes() - Static method in class sc.fiji.snt.analysis.ProfileProcessor

Gets the array of available ProfileProcessor.Shapes

getShollAnalyzer() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getShollAnalyzer() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the ShollAnalyzer instance associated with this TreeStatistics instance.

getShollDecay() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getShollMetric(String) - Method in class sc.fiji.snt.analysis.TreeStatistics

getShortestPath(SWCPoint, SWCPoint) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Gets the shortest path between source and target vertex as a Path object.

getShortestPathVertices(SWCPoint, SWCPoint) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Gets the shortest path between source and target vertex as a Deque of SWCPoint objects.

getShortName() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo

getSimplifiedGraph() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Returns a simplified graph in which slab nodes are removed and the graph is represented only by root, branch nodes and leaves.

getSimplifiedGraph(DirectedWeightedGraph) - Static method in class sc.fiji.snt.analysis.graph.GraphUtils

Deprecated.

getSingleGraph() - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Generates a single DirectedWeightedGraphs by combining BinaryTracer.getGraphs()'s list into a single, combined graph.

getSinglePane() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

getSingleSelectedPath() - Method in class sc.fiji.snt.SNT

getSingleTree() - Method in class sc.fiji.snt.PathManagerUI

getSingleTree() - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Generates a single Tree from BinaryTracer.getSingleGraph().

getSingleValueMetrics() - Static method in class sc.fiji.snt.analysis.MultiTreeColorMapper

Gets the list of single-value mapping metrics.

getSingleValueMetrics() - Method in class sc.fiji.snt.analysis.ShollAnalyzer

getSize() - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

Gets the size (area or volume) of the convex hull, which is the area for 2D hulls or the volume for 3D hulls.

getSize() - Method in class sc.fiji.snt.PathNodeCanvas

getSkeleton() - Method in class sc.fiji.snt.Tree

Retrieves the rasterized skeleton of this tree at 1:1 scaling.

getSkeleton(int) - Method in class sc.fiji.snt.Tree

Retrieves the rasterized skeleton of this tree at 1:1 scaling.

getSkeleton2D() - Method in class sc.fiji.snt.Tree

Retrieves a 2D projection of the rasterized skeleton of this tree at 1:1 scaling.

getSkeleton2D(int) - Method in class sc.fiji.snt.Tree

Retrieves a 2D projection of the rasterized skeleton of this tree at 1:1 scaling.

getSkewness() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getSkewness(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Calculates the skewness.

getSlabZMax() - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

getSlabZMin() - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

getSlice() - Method in class sc.fiji.snt.PathNodeCanvas

getSlice(int) - Method in class sc.fiji.snt.tracing.image.SearchImageStack

getSliceLabels(ImageStack) - Static method in class sc.fiji.snt.util.ImpUtils

getSlope() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getSmoothedPath(int) - Method in class sc.fiji.snt.Path

Returns a smoothed version of this path using a simple moving average filter.

getSnapSize() - Method in class sc.fiji.snt.gui.ComponentMover

Get the snap size

getSNT() - Method in class sc.fiji.snt.PathManagerUI

Gets the SNT instance associated with this Path Manager.

getSomaCompartment() - Method in class sc.fiji.snt.io.MouseLightLoader

Gets the brain compartment containing the soma.

getSomaLocation() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo

getSomaLocation() - Method in class sc.fiji.snt.io.MouseLightLoader

Gets the soma location for this neuron.

getSomaNodes() - Method in class sc.fiji.snt.Tree

Gets the list of all nodes tagged as Path.SWC_SOMA.

getSomaRenderMode() - Static method in class sc.fiji.snt.PathNodeCanvas

Gets the current rendering mode for soma nodes.

getSomaRoi() - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Gets the current soma ROI.

getSource() - Method in class sc.fiji.snt.analysis.graph.AnnotationWeightedEdge

getSource() - Method in class sc.fiji.snt.analysis.graph.SWCWeightedEdge

getSource(int, int) - Method in class sc.fiji.snt.io.SpimDataUtils.CalibratedSource

getSourceAnnotation() - Method in class sc.fiji.snt.viewer.OBJMesh

Returns the BrainAnnotation (atlas compartment) from which this mesh was retrieved, or null if this mesh was loaded from a standalone file.

getSourceGraph() - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter

getSourcePaths() - Method in class sc.fiji.snt.Fill

Returns the set of source paths for the filled structure.

getSourcePathsStringHuman() - Method in class sc.fiji.snt.Fill

getSourcePathsStringMachine() - Method in class sc.fiji.snt.Fill

getSources() - Method in class sc.fiji.snt.viewer.BvvMultiSource

getSpacing() - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Gets the voxel spacing used by this tracer.

getSpacing() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

getSpacing(ImagePlus, int) - Static method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

getSpacing(ImgPlus<?>) - Static method in class sc.fiji.snt.util.ImgUtils

Extracts voxel spacing from ImgPlus axis metadata.

getSpacingUnits() - Method in class sc.fiji.snt.io.NeurolucidaImporter

Returns the spacing units string (default "um").

getSpacingUnits() - Method in class sc.fiji.snt.SNT

getSpacingUnits(ImgPlus<?>) - Static method in class sc.fiji.snt.util.ImgUtils

Extracts spacing units from an ImgPlus.

getSparseGraph() - Method in class sc.fiji.snt.Tree

Assembles a memory-efficient CSR-backed DirectedWeightedGraph from this Tree.

getSpatialUnit() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getSpatialUnit() - Method in class sc.fiji.snt.analysis.TreeStatistics

getSpeciesCommonName() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo

getSpeciesID() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo

getSpeciesNeuronIDs(int) - Static method in class sc.fiji.snt.annotation.InsectBrainUtils

getSpeciesScientificName() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo

getSpineOrVaricosityCount() - Method in class sc.fiji.snt.Path

Gets the number of spines or varicosities associated with this path.

getSpineOrVaricosityDensity() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the overall density of spines/varicosities associated with this tree

getSpinner() - Method in class sc.fiji.snt.gui.CheckboxSpinner

getStandardizedCompartment(String) - Static method in interface sc.fiji.snt.TreeProperties

getStandardizedMetric(String) - Static method in class sc.fiji.snt.analysis.NodeStatistics

getStartJoins() - Method in class sc.fiji.snt.Path

Deprecated.

use Path.getParentPath() instead

getStartJoinsPoint() - Method in class sc.fiji.snt.Path

Deprecated.

Use Path.getBranchPoint() instead.

NB: Earlier versions of Simple Neurite Tracer allowed paths to connect at either the start point (getStartJoinsPoint()) or end-point (getStartJoinsPoint()). Useful for some applications but a huge headache to handle.

getState() - Method in class sc.fiji.snt.SNTUI

Gets the current UI state.

getState(boolean) - Method in class sc.fiji.snt.tracing.BiSearchNode

getState(long) - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

getState(long) - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

getState(long) - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

getState(long) - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Get Fast Marching state at linear index.

getStateFromGoal() - Method in class sc.fiji.snt.tracing.BiSearchNode

getStateFromStart() - Method in class sc.fiji.snt.tracing.BiSearchNode

getStatistics(boolean) - Method in class sc.fiji.snt.SNTService

Returns a TreeStatistics instance constructed from current Paths.

getStats() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

getStats() - Method in class sc.fiji.snt.SNT

getStatsSecondary() - Method in class sc.fiji.snt.SNT

getStatusSummary() - Method in class sc.fiji.snt.CurationManager

Generates a summary string for the status bar: shows the most severe warning, suitable for display in the QUERY_KEEP status text.

getStrahlerAnalyzer() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getStrahlerAnalyzer() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the StrahlerAnalyzer instance associated with this TreeStatistics instance

getStrahlerBifurcationRatio() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the average Strahler bifurcation ratio of analyzed tree.

getStrahlerNumber() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the highest Strahler number of the analyzed tree.

getString(String, String, String) - Method in class sc.fiji.snt.gui.GuiUtils

getStrings(String, String[], String[]) - Method in class sc.fiji.snt.gui.GuiUtils

getStrings(String, Map<String, List<String>>, String...) - Method in class sc.fiji.snt.gui.GuiUtils

getStringSet(String, String, Collection<String>) - Method in class sc.fiji.snt.gui.GuiUtils

getStructureIdPath() - Method in class sc.fiji.snt.annotation.AllenCompartment

getSubgraph(Set<SWCPoint>) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Returns the subgraph defined by the supplied subset of vertices, including their edges.

getSucceeded() - Method in class sc.fiji.snt.PathFitter

Checks whether the fit succeeded.

getSum() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getSum(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Calculates the sum.

getSummaries() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCalibrator.CalibrationResult

getSummary() - Method in class sc.fiji.snt.tracing.auto.AutoTraceConfig

Returns a human-readable summary of the derived configuration, suitable for display in a dialog or log.

getSummaryRow() - Method in class sc.fiji.snt.analysis.SNTTable

getSummaryStatistics() - Method in class sc.fiji.snt.analysis.growth.GrowthAnalysisResults

Gets summary statistics for all analyzed neurites.

getSummaryStats(String) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getSummaryStats(String) - Method in class sc.fiji.snt.analysis.PathStatistics

getSummaryStats(String) - Method in class sc.fiji.snt.analysis.TreeStatistics

Computes the SummaryStatistics for the specified measurement.

getSummaryTable() - Method in class sc.fiji.snt.plugin.RootAngleAnalyzerCmd

Gets the summary table containing the tabular results of the analysis.

getSummaryTable() - Method in class sc.fiji.snt.plugin.StrahlerCmd

Gets the summary table containing the tabular results of the analysis.

getSumSq() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getSumSq(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Calculates the sum of the squared values.

getSWC() - Method in class sc.fiji.snt.io.MouseLightLoader

Gets all the data associated with this reconstruction in the SWC format.

getSWCcolor(int) - Static method in class sc.fiji.snt.Path

Gets the default SWC colors used by SNT.

getSWCFileForIndex(String, int) - Method in class sc.fiji.snt.PathAndFillManager

getSWCFor(Collection<Path>) - Method in class sc.fiji.snt.PathAndFillManager

Converts a collection of connected Path objects into SWC points for export.

getSWCType() - Method in class sc.fiji.snt.Path

Gets the SWC type.

getSWCTypeMap() - Static method in class sc.fiji.snt.Tree

Returns the SWC Type flags used by SNT.

getSWCtypeName(int, boolean) - Static method in class sc.fiji.snt.Path

Gets the SWC type label associated with the specified type flag.

getSWCtypeNames() - Static method in class sc.fiji.snt.Path

Gets the list of string representations of SWC types

getSWCTypeNames(boolean) - Method in class sc.fiji.snt.Tree

Gets the set of SWC type labels present in this tree with optional soma inclusion in a readable form.

getSWCtypes() - Static method in class sc.fiji.snt.Path

Gets the list of SWC types.

getSWCTypes() - Method in class sc.fiji.snt.Tree

Extracts the SWC-type flags present in this Tree.

getSWCTypes(boolean) - Method in class sc.fiji.snt.Tree

Gets the set of SWC types present in this tree with optional soma inclusion.

getSWCTypesAsString() - Method in class sc.fiji.snt.analysis.TreeStatistics

getSymmetryAxis() - Method in class sc.fiji.snt.viewer.OBJMesh

getSystemClipboard(boolean) - Static method in class sc.fiji.snt.util.ImpUtils

Retrieves an ImagePlus from the system clipboard

getTab(int) - Method in class sc.fiji.snt.gui.OntologyBrowser

Returns the tab at the given index.

getTabbedPane() - Static method in class sc.fiji.snt.gui.GuiUtils

getTabCount() - Method in class sc.fiji.snt.gui.OntologyBrowser

Returns the number of ontology tabs.

getTable() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the table currently being used by this TreeStatistics instance

getTable() - Method in class sc.fiji.snt.PathManagerUI

getTable() - Method in class sc.fiji.snt.plugin.StrahlerCmd

Deprecated.

Use StrahlerCmd.getSummaryTable() instead

getTable() - Method in class sc.fiji.snt.SNTService

Returns a reference to SNT's main table of measurements.

getTable() - Method in class sc.fiji.snt.SNTUI

getTable(Path) - Method in class sc.fiji.snt.analysis.NodeProfiler

getTable(Path, int) - Method in class sc.fiji.snt.analysis.NodeProfiler

getTaggedGraph() - Method in class sc.fiji.snt.analysis.RootAngleAnalyzer

getTaggedTree() - Method in class sc.fiji.snt.analysis.RootAngleAnalyzer

getTaggedTree(String, double, double) - Method in class sc.fiji.snt.analysis.RootAngleAnalyzer

Returns a recolored copy of the analyzed tree with the root angles assigned to its node values.

getTaggedTree(ColorTable) - Method in class sc.fiji.snt.analysis.RootAngleAnalyzer

Returns a recolored copy of the analyzed tree with the root angles assigned to its node values.

getTaggedTree(ColorTable, double, double) - Method in class sc.fiji.snt.analysis.RootAngleAnalyzer

Returns a recolored copy of the analyzed tree with the root angles assigned to its node values.

getTags() - Method in class sc.fiji.snt.util.SWCPoint

Gets the tags associated with this point.

getTangent() - Method in class sc.fiji.snt.Path.PathNode

getTangent(int, int, double[]) - Method in class sc.fiji.snt.Path

getTarget() - Method in class sc.fiji.snt.analysis.graph.AnnotationWeightedEdge

getTarget() - Method in class sc.fiji.snt.analysis.graph.SWCWeightedEdge

getTemp(String, boolean) - Method in class sc.fiji.snt.SNTPrefs

Gets a temporary boolean preference value that will be cleared at session end.

getTemp(String, String) - Method in class sc.fiji.snt.SNTPrefs

Gets a temporary string preference value that will be cleared at session end.

getTerminalBranches() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getTerminalBranches() - Method in class sc.fiji.snt.analysis.PathStatistics

Gets the terminal branches from the analyzed paths.

getTerminalBranches() - Method in class sc.fiji.snt.analysis.TreeStatistics

Retrieves the terminal branches of the analyzed Tree.

getTerminalLength() - Method in class sc.fiji.snt.analysis.PathStatistics

Gets the total length of terminal branches.

getTerminalLength() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the cable length of terminal branches

getThicknessMultiplier() - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Gets the thickness multiplier for path rendering.

getThreads() - Static method in class sc.fiji.snt.SNTPrefs

Gets the current number of threads setting.

getThreeNumbers(String, String, Number[], String[], int) - Method in class sc.fiji.snt.gui.GuiUtils

getThreshold() - Method in class sc.fiji.snt.analysis.graph.AnnotationGraph

getThreshold() - Method in class sc.fiji.snt.Fill

getThreshold() - Method in class sc.fiji.snt.tracing.FillerThread

getTimePointCount() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the number of unique time points in the series.

getTimePointEntryCount() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the total number of time point entries in the series (including duplicates).

getTimePoints() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the time series data points for this neurite.

getTimeStamp() - Static method in class sc.fiji.snt.SNTUtils

getTimeUnits() - Method in class sc.fiji.snt.analysis.growth.GrowthAnalysisResults

Gets the time units used in the analysis.

getTipExtensionDistance() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Returns the maximum distance (in voxels) for A*-based tip extension.

getTips() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Gets the end points (tips) of the graph.

getTips() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph

Gets the end points (tips) of the subgraph.

getTips() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

getTips() - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the position of all the tips in the analyzed tree.

getTips() - Method in class sc.fiji.snt.Tree

Gets the end points (tips) of the graph.

getTips(double) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the position of all tips in the analyzed tree that are further distant than the specified distance from the root.

getTips(double, double) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the position of all tips in the analyzed tree that are within the specified distance range from the root.

getTips(BrainAnnotation) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the position of all the tips in the analyzed tree associated with the specified annotation.

getTips(BrainAnnotation, boolean) - Method in class sc.fiji.snt.analysis.TreeStatistics

Gets the position of all the tips in the analyzed tree associated with the specified annotation.

getTitle() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollTable

getTitle() - Method in class sc.fiji.snt.analysis.SNTChart

getTitle() - Method in class sc.fiji.snt.analysis.SNTTable

Gets the title of the table.

getTitle() - Method in class sc.fiji.snt.viewer.Viewer2D

Gets the plot display title.

getToolTipForCell(Object) - Method in class sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter

getToolTipForCell(Object) - Method in class sc.fiji.snt.viewer.geditor.TreeGraphAdapter

getTopologicalOrderIterator() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Gets a TopologicalOrderIterator for this graph.

getTotalDuration(double) - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the total duration of the time series.

getTotalElongationLength() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the total length gained from elongation events.

getTotalGrowth() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the total growth (final length - initial length).

getTotalPhaseCount() - Method in class sc.fiji.snt.analysis.growth.GrowthAnalysisResults

Gets the total number of growth phases across all neurites.

getTotalRetractionLength() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Gets the total length lost to retraction events.

getTracedRegionBuffer() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Returns the buffer size (in voxels) applied around traced regions between multi-soma passes.

getTracingCanvas() - Method in class sc.fiji.snt.SNT

getTracingCanvasPopupMenu() - Method in class sc.fiji.snt.SNTUI

getTransparency() - Method in class sc.fiji.snt.seed.SeedOverlay

getTransparency() - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Gets the transparency level for path rendering.

getTree() - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

Gets the tree being analyzed.

getTree() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Returns a new tree associated with this graph, using the current state of the graph to build the tree.

getTree() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph

Returns the tree associated with the parent's graph

getTree() - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

Returns the tree associated with this parser

getTree() - Method in class sc.fiji.snt.gui.OntologyBrowser.OntologyTab

Returns the underlying checkbox tree.

getTree() - Method in class sc.fiji.snt.io.InsectBrainLoader

Gets the collection of Paths for the specified cell ID

getTree() - Method in class sc.fiji.snt.io.MouseLightLoader

Script-friendly method to extract the entire neuron as a collection of Paths.

getTree() - Method in class sc.fiji.snt.SNTService

Gets the collection of paths listed in the Path Manager as a Tree object.

getTree(boolean) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Returns a tree associated with this graph.

getTree(boolean) - Method in class sc.fiji.snt.SNTService

Gets the collection of paths listed in the Path Manager as a Tree object.

getTree(int) - Method in class sc.fiji.snt.PathAndFillManager

Returns the specified Tree.

getTree(String) - Method in class sc.fiji.snt.io.FlyCircuitLoader

Gets the collection of Paths for the specified cell ID

getTree(String) - Method in class sc.fiji.snt.io.MouseLightLoader

Script-friendly method to extract a compartment as a collection of Paths.

getTree(String) - Method in class sc.fiji.snt.io.NeuroMorphoLoader

Gets the collection of Paths for the specified cell ID

getTree(String) - Method in interface sc.fiji.snt.io.RemoteSWCLoader

getTree(String) - Method in class sc.fiji.snt.PathAndFillManager

Returns the specified Tree.

getTree(String) - Method in class sc.fiji.snt.viewer.Viewer3D

Gets the tree associated with the specified label.

getTree(String, ColorRGB) - Method in class sc.fiji.snt.io.MouseLightLoader

Extracts a cell compartment as a collection of Paths.

getTreeAsSceneryNode(Tree) - Method in class sc.fiji.snt.SciViewSNT

Gets the specified Tree as a Scenery Node.

getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class sc.fiji.snt.gui.OntologyBrowser.AllenCCFRenderer

getTreeCount() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCalibrator.CalibrationResult

getTreeID() - Method in class sc.fiji.snt.Path

Gets the identifier of the Tree associated to this Path (if any).

getTreeLabel() - Method in class sc.fiji.snt.Path

getTreeModel() - Static method in class sc.fiji.snt.annotation.DrosophilaUtils

Builds a DefaultTreeModel representing the Drosophila adult brain ontology hierarchy.

getTreeModel(boolean) - Static method in class sc.fiji.snt.annotation.AllenUtils

Retrieves the Allen CCF hierarchical tree data.

getTreePath() - Method in class sc.fiji.snt.annotation.AllenCompartment

Gets the tree path of this compartment.

getTrees() - Method in class sc.fiji.snt.analysis.graph.AnnotationGraph

getTrees() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Return the connected components of this graph as a list of Trees

getTrees() - Method in class sc.fiji.snt.gui.DemoRunner.Demo

getTrees() - Method in class sc.fiji.snt.io.NDFImporter

Extracts tracings from the specified file path

getTrees() - Method in class sc.fiji.snt.io.NeurolucidaImporter

Returns the parsed trees (one per <tree> element in the file).

getTrees() - Method in class sc.fiji.snt.PathAndFillManager

Returns all the paths associated with this PathAndFillManager instance, grouped by Tree.

getTrees() - Method in class sc.fiji.snt.SNTService

Gets the collection of paths listed in the Path Manager as a Tree object.

getTrees() - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Generates a list of Trees from the skeleton image.

getTrees() - Method in class sc.fiji.snt.viewer.Viewer3D

Returns all trees added to this viewer.

getTrees(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Returns all trees added to this viewer.

getTreeWithSamePathStructure() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Attempt to build a new Tree with the same Path hierarchy as the source Tree.

getTwoChoices(String, String, String[], String, String, String[], String) - Method in class sc.fiji.snt.gui.GuiUtils

getTwoNumbers(String, String, Number[], String[], int) - Method in class sc.fiji.snt.gui.GuiUtils

getType() - Method in class sc.fiji.snt.event.SNTEvent

Gets the type of this SNT event.

getType() - Method in class sc.fiji.snt.PathNodeCanvas

Returns the type of node.

getType() - Method in class sc.fiji.snt.viewer.Annotation3D

Gets the type of this annotation.

getUI() - Method in class sc.fiji.snt.SNT

Gets the main UI.

getUI() - Method in class sc.fiji.snt.SNTService

Returns a reference to SNT's UI.

getUIState() - Method in class sc.fiji.snt.SNT

getUndoManager() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

getUnfitted() - Method in class sc.fiji.snt.Path

Gets the original (unfitted) path that this path is a fitted version of.

getUniquelySuffixedFile(File) - Static method in class sc.fiji.snt.SNTUtils

getUniquelySuffixedFile(File, String) - Static method in class sc.fiji.snt.SNTUtils

getUniquelySuffixedTifFile(File) - Static method in class sc.fiji.snt.SNTUtils

getUnit() - Method in class sc.fiji.snt.util.BoundingBox

Gets the length unit of voxel spacing

getUnit(String) - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

Returns the physical unit associated with the specified metric.

getUnit(String) - Method in class sc.fiji.snt.analysis.TreeStatistics

Returns the physical unit associated with the specified metric.

getUnscaledNodes() - Method in class sc.fiji.snt.Path

getUnscaledNodesInViewPort(TracerCanvas) - Method in class sc.fiji.snt.Path

getUnscaledPoint() - Method in class sc.fiji.snt.util.PointInImage

Converts the coordinates of this point into pixel units if this point is associated with a Path.

getUnscaledPoint(int) - Method in class sc.fiji.snt.util.PointInImage

Converts the coordinates of this point into pixel units if this point is associated with a Path.

getUnSelectedPathsRenderedInViewPort(TracerCanvas) - Method in class sc.fiji.snt.PathAndFillManager

getUseFitted() - Method in class sc.fiji.snt.Path

Gets whether the fitted 'flavor' of this Path is in use.

getUseSubVolumeStats() - Method in class sc.fiji.snt.SNT

getUUID() - Method in class sc.fiji.snt.annotation.AllenCompartment

getValidTrees() - Method in class sc.fiji.snt.plugin.StrahlerCmd

Returns the Tree(s) successfully parsed (i.e., topologically valid)

getValue() - Method in class sc.fiji.snt.gui.CheckboxSpinner

getValue(int, int) - Method in class sc.fiji.snt.tracing.image.ArraySearchImage

getValue(int, int) - Method in class sc.fiji.snt.tracing.image.ListSearchImage

getValue(int, int) - Method in class sc.fiji.snt.tracing.image.MapSearchImage

getValue(int, int) - Method in interface sc.fiji.snt.tracing.image.SearchImage

getValueAt(int, int) - Method in class sc.fiji.snt.seed.SeedTableModel

getValues() - Method in class sc.fiji.snt.analysis.ProfileProcessor

The profile values, or null if they have not been processed yet.

getValues(Path) - Method in class sc.fiji.snt.analysis.NodeProfiler

Gets the profile for the specified path as a map of lists of pixel intensities (profile indices as keys)

getValues(Path) - Method in class sc.fiji.snt.analysis.PathProfiler

Gets the profile for the specified path as a map of lists, with distances (or indices) stored under PathProfiler.X_VALUES ("x-values") and intensities under PathProfiler.Y_VALUES ("y-values").

getValues(Path, int) - Method in class sc.fiji.snt.analysis.PathProfiler

Gets the profile for the specified path as a map of lists, with distances (or indices) stored under PathProfiler.X_VALUES ("x-values") and intensities under PathProfiler.Y_VALUES ("y-values").

getValues(Path, int, int) - Method in class sc.fiji.snt.analysis.NodeProfiler

Gets the profile for the specified path as a map of lists of pixel intensities (profile indices as keys)

getVariance() - Method in class sc.fiji.snt.analysis.PCAnalyzer.PrincipalAxis

getVariance() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getVariance(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Calculates the variance.

getVariancePercentage(double) - Method in class sc.fiji.snt.analysis.PCAnalyzer.PrincipalAxis

Computes the percentage of total variance explained by this principal axis.

getVariancePercentages(PCAnalyzer.PrincipalAxis[]) - Static method in class sc.fiji.snt.analysis.PCAnalyzer

Computes the variance percentages for an array of principal axes.

getVariancePercentages(PCAnalyzer.PrincipalAxis[]) - Static method in class sc.fiji.snt.analysis.PCAnalyzer.PrincipalAxis

Computes the variance percentages for an array of principal axes.

getVertexColor(V) - Method in class sc.fiji.snt.analysis.graph.SNTGraph

getVertexColorRGBMap() - Method in class sc.fiji.snt.analysis.graph.SNTGraph

getVertexValue(V) - Method in class sc.fiji.snt.analysis.graph.SNTGraph

getVertexValueMap() - Method in class sc.fiji.snt.analysis.graph.SNTGraph

getVertices() - Method in class sc.fiji.snt.viewer.OBJMesh

Returns the mesh vertices.

getVertices(String) - Method in class sc.fiji.snt.viewer.OBJMesh

Returns the mesh vertices.

getViewer() - Method in class sc.fiji.snt.viewer.Bvv

getViewerFrame() - Method in class sc.fiji.snt.viewer.Bvv

getViewerPanel() - Method in class sc.fiji.snt.viewer.Bvv

getViewers() - Static method in class sc.fiji.snt.SNTUtils

getViewPort() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

getVolume() - Method in class sc.fiji.snt.Fill

Returns the Fill volume.

getVolume() - Method in class sc.fiji.snt.viewer.Annotation3D

getVolume() - Method in class sc.fiji.snt.viewer.OBJMesh

Gets the volume of this mesh.

getVoxelDimensions() - Method in class sc.fiji.snt.io.SpimDataUtils.CalibratedSource

getWeight() - Method in class sc.fiji.snt.analysis.graph.AnnotationWeightedEdge

getWeight() - Method in class sc.fiji.snt.analysis.graph.SWCWeightedEdge

getWidth() - Method in class sc.fiji.snt.analysis.TreeStatistics

Returns the width of the BoundingBox box of the tree being measured

getWidth() - Method in class sc.fiji.snt.SNT

getWindowSizeFraction() - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Gets the current window size fraction for change point detection.

getWorkspaceDir() - Method in class sc.fiji.snt.SNTPrefs

getX() - Method in class sc.fiji.snt.analysis.PCAnalyzer.PrincipalAxis

getX() - Method in class sc.fiji.snt.seed.SeedPoint

getX() - Method in class sc.fiji.snt.tracing.BiSearchNode

getX() - Method in class sc.fiji.snt.tracing.DefaultSearchNode

getX() - Method in interface sc.fiji.snt.tracing.SearchNode

getX() - Method in class sc.fiji.snt.util.PointInImage

getX() - Method in interface sc.fiji.snt.util.SNTPoint

getX() - Method in class sc.fiji.snt.util.SWCPoint

getXUnscaled(int) - Method in class sc.fiji.snt.Path

Returns the unscaled X position of a node.

getXUnscaledDouble(int) - Method in class sc.fiji.snt.Path

getXValues() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Returns the abscissae of the sampled linear plot for sampled data.

getXValues() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

Returns the abscissae of the Semi-log /Log-log plot for sampled data.

getXValues() - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

getXValues() - Method in interface sc.fiji.snt.analysis.sholl.math.ShollStats

getXYPlot() - Method in class sc.fiji.snt.analysis.PathProfiler

Gets the plot profile as an PlotService plot.

getXYPlot(int) - Method in class sc.fiji.snt.analysis.PathProfiler

Gets the plot profile as an PlotService plot.

getXYZCImage(ImagePlus) - Static method in class sc.fiji.snt.util.ImgUtils

Gets a 4D (X, Y, Z, C) view of the ImagePlus at the current time frame, retaining all channels.

getXYZLabels() - Static method in class sc.fiji.snt.annotation.AllenUtils

getXYZLabels() - Static method in class sc.fiji.snt.annotation.VFBUtils

getXYZLabels() - Static method in class sc.fiji.snt.annotation.ZBAtlasUtils

getY() - Method in class sc.fiji.snt.analysis.PCAnalyzer.PrincipalAxis

getY() - Method in class sc.fiji.snt.seed.SeedPoint

getY() - Method in class sc.fiji.snt.tracing.BiSearchNode

getY() - Method in class sc.fiji.snt.tracing.DefaultSearchNode

getY() - Method in interface sc.fiji.snt.tracing.SearchNode

getY() - Method in class sc.fiji.snt.util.PointInImage

getY() - Method in interface sc.fiji.snt.util.SNTPoint

getY() - Method in class sc.fiji.snt.util.SWCPoint

getYUnscaled(int) - Method in class sc.fiji.snt.Path

Returns the unscaled Y position of a node.

getYUnscaledDouble(int) - Method in class sc.fiji.snt.Path

getYValues() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Returns the ordinates of the sampled linear plot of sampled data.

getYValues() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

Returns the ordinates of the Semi-log/Log-log plot for sampled data.

getYValues() - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

getYValues() - Method in interface sc.fiji.snt.analysis.sholl.math.ShollStats

getYValues(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

getYValues(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

getYValues(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

getYValues(boolean) - Method in interface sc.fiji.snt.analysis.sholl.math.ShollStats

getZ() - Method in class sc.fiji.snt.analysis.PCAnalyzer.PrincipalAxis

getZ() - Method in class sc.fiji.snt.seed.SeedPoint

getZ() - Method in class sc.fiji.snt.tracing.BiSearchNode

getZ() - Method in class sc.fiji.snt.tracing.DefaultSearchNode

getZ() - Method in interface sc.fiji.snt.tracing.SearchNode

getZ() - Method in class sc.fiji.snt.util.PointInImage

getZ() - Method in interface sc.fiji.snt.util.SNTPoint

getZ() - Method in class sc.fiji.snt.util.SWCPoint

getZattrsPath(String, String, int) - Static method in class sc.fiji.snt.io.OmeAxisUtils

Get the path to .zattrs containing multiscales metadata.

getZFudge() - Method in class sc.fiji.snt.tracing.cost.OneMinusErf

getZplaneROIs(int) - Method in class sc.fiji.snt.analysis.RoiConverter

Extracts all the ROIs converted so far associated with the specified Z-plane.

getZplaneROIs(Overlay, int) - Static method in class sc.fiji.snt.analysis.RoiConverter

Extracts ROIs associated with a specified Z position.

getZUnscaled(int) - Method in class sc.fiji.snt.Path

Returns the unscaled Z position of a node.

getZUnscaledDouble(int) - Method in class sc.fiji.snt.Path

getZYXZ(ImagePlus, int) - Static method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

glasbeyColorsAWT(int) - Static method in class sc.fiji.snt.util.ColorMaps

GLASSES - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

GLOBE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

goal_x - Variable in class sc.fiji.snt.tracing.BiSearch

goal_y - Variable in class sc.fiji.snt.tracing.BiSearch

goal_z - Variable in class sc.fiji.snt.tracing.BiSearch

GRADUATION_CAP - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

graph - Variable in class sc.fiji.snt.analysis.graph.GraphColorMapper

GRAPH_DIAMETER - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Longest shortest path: Length" statistics.

GRAPH_DIAMETER_ANGLE - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Longest shortest path: Extension angle" statistics.

GRAPH_DIAMETER_ANGLE_XY - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Longest shortest path: Extension angle XY" statistics.

GRAPH_DIAMETER_ANGLE_XZ - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Longest shortest path: Extension angle XZ" statistics.

GRAPH_DIAMETER_ANGLE_ZY - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Longest shortest path: Extension angle ZY" statistics.

GraphAdapterMapperCmd - Class in sc.fiji.snt.plugin

Command for mapping colors to graph nodes and edges based on specified properties and visualization parameters.

GraphAdapterMapperCmd() - Constructor for class sc.fiji.snt.plugin.GraphAdapterMapperCmd

GraphColorMapper<V,E> - Class in sc.fiji.snt.analysis.graph

A color mapping utility for graph visualization that assigns colors to vertices and edges based on various graph metrics.

GraphColorMapper() - Constructor for class sc.fiji.snt.analysis.graph.GraphColorMapper

GraphColorMapper(Context) - Constructor for class sc.fiji.snt.analysis.graph.GraphColorMapper

graphComponent - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor

GraphEditor - Class in sc.fiji.snt.viewer.geditor

Main editor panel for interactive visualization and manipulation of SNT graphs.

GraphEditor(String, mxGraphComponent) - Constructor for class sc.fiji.snt.viewer.geditor.GraphEditor

GraphGeneratorCmd - Class in sc.fiji.snt.gui.cmds

Command for displaying the contents of Path Manager in the "SNT Graph Viewer"

GraphGeneratorCmd() - Constructor for class sc.fiji.snt.gui.cmds.GraphGeneratorCmd

graphLayout(String) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

Creates an action that executes the specified layout.

graphOrder() - Method in class sc.fiji.snt.annotation.AllenCompartment

graphOutline - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor

GraphUtils - Class in sc.fiji.snt.analysis.graph

Utilities for Graph handling.

GraphViewer - Class in sc.fiji.snt.viewer

Provides a graphical user interface for visualizing and interacting with graphs using SNT's "Graph Viewer".

GraphViewer(SNTGraph<?, ? extends DefaultWeightedEdge>) - Constructor for class sc.fiji.snt.viewer.GraphViewer

Constructs a new GraphViewer for the specified graph.

GRID - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

GroupAnalyzerCmd - Class in sc.fiji.snt.plugin

Command for Comparing Groups of Tree(s).

GroupAnalyzerCmd() - Constructor for class sc.fiji.snt.plugin.GroupAnalyzerCmd

GroupedTreeStatistics - Class in sc.fiji.snt.analysis

Computes statistics from Tree groups.

GroupedTreeStatistics() - Constructor for class sc.fiji.snt.analysis.GroupedTreeStatistics

Instantiates a new grouped tree statistics.

GrowthAnalysisResults - Class in sc.fiji.snt.analysis.growth

Container class for growth analysis results from GrowthAnalyzer, serving as the primary interface for accessing growth analysis results.

GrowthAnalysisResults(Map<String, NeuriteGrowthData>, double, String) - Constructor for class sc.fiji.snt.analysis.growth.GrowthAnalysisResults

Creates a new GrowthAnalysisResults container.

GrowthAnalysisResults.GrowthSummaryStatistics - Record Class in sc.fiji.snt.analysis.growth

Container for summary statistics across all analyzed neurites.

GrowthAnalysisResults.NeuriteSelectionCriterion - Interface in sc.fiji.snt.analysis.growth

Interface for defining neurite selection criteria.

GrowthAnalyzer - Class in sc.fiji.snt.analysis.growth

Core analyzer for time-lapse growth analysis of neuronal paths.

GrowthAnalyzer() - Constructor for class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Creates a new GrowthAnalyzer with default parameters.

GrowthAnalyzer(double, double, double) - Constructor for class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Creates a new GrowthAnalyzer with custom threshold parameters.

GrowthAnalyzer.ElongationEvent - Record Class in sc.fiji.snt.analysis.growth

Represents an elongation event

GrowthAnalyzer.GrowthPhase - Record Class in sc.fiji.snt.analysis.growth

Represents a growth phase with specific characteristics

GrowthAnalyzer.GrowthPhaseType - Enum Class in sc.fiji.snt.analysis.growth

Types of growth phases

GrowthAnalyzer.RetractionEvent - Record Class in sc.fiji.snt.analysis.growth

Represents a retraction event

GrowthAnalyzer.TimePoint - Record Class in sc.fiji.snt.analysis.growth

Represents a single time point measurement

GrowthAnalyzerCmd - Class in sc.fiji.snt.plugin

GUI command to the GrowthAnalyzer class.

GrowthAnalyzerCmd() - Constructor for class sc.fiji.snt.plugin.GrowthAnalyzerCmd

GrowthPhase(int, int, double, double, double, double, double, GrowthAnalyzer.GrowthPhaseType) - Constructor for record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhase

Creates an instance of a GrowthPhase record class.

GrowthSummaryStatistics() - Constructor for record class sc.fiji.snt.analysis.growth.GrowthAnalysisResults.GrowthSummaryStatistics

GrowthSummaryStatistics(double, double, double, double, double, int, int, int) - Constructor for record class sc.fiji.snt.analysis.growth.GrowthAnalysisResults.GrowthSummaryStatistics

Creates an instance of a GrowthSummaryStatistics record class.

GUESS_SLOG - Static variable in interface sc.fiji.snt.analysis.sholl.math.ShollStats

Flag for automatic choice between Semi-log/Log-log analysis

guessResamplingFactor() - Method in class sc.fiji.snt.SNT

guessTracesFileType(String) - Method in class sc.fiji.snt.PathAndFillManager

guiUtils - Variable in class sc.fiji.snt.PathManagerUI

guiUtils - Variable in class sc.fiji.snt.SNTUI

GuiUtils - Class in sc.fiji.snt.gui

Misc. utilities for SNT's GUI.

GuiUtils() - Constructor for class sc.fiji.snt.gui.GuiUtils

Create a new GuiUtils instance using active (focused) window as parent.

GuiUtils(Component) - Constructor for class sc.fiji.snt.gui.GuiUtils

GuiUtils.Buttons - Class in sc.fiji.snt.gui

GuiUtils.Buttons.OptionsButton - Class in sc.fiji.snt.gui

GuiUtils.JTables - Class in sc.fiji.snt.gui

Utility methods for JTable configuration and creation.

GuiUtils.JTables.DetachableTable - Class in sc.fiji.snt.gui

Stateful helper that extracts a JScrollPane from its current parent into a free-floating, modeless JDialog, and re-attaches it on demand.

GuiUtils.JTables.VisitingZoom - Class in sc.fiji.snt.gui

Stateful "visiting zoom" helper used by table panels that navigate the canvas on double-click (BookmarkManager, CurationManager, SeedOverlayPanel).

GuiUtils.JTrees - Class in sc.fiji.snt.gui

GuiUtils.MenuItems - Class in sc.fiji.snt.gui

GuiUtils.SplitPanes - Class in sc.fiji.snt.gui

GWDTMultiSomaCmd - Class in sc.fiji.snt.plugin

Interactive command for multi-soma GWDT autotracing.

GWDTMultiSomaCmd() - Constructor for class sc.fiji.snt.plugin.GWDTMultiSomaCmd

GWDTMultiSomaCommonCmd - Class in sc.fiji.snt.plugin

Abstract base for multi-soma GWDT autotracing commands.

GWDTMultiSomaCommonCmd() - Constructor for class sc.fiji.snt.plugin.GWDTMultiSomaCommonCmd

GWDTMultiSomaFileCmd - Class in sc.fiji.snt.plugin

Non-interactive command for file-based multi-soma GWDT autotracing with support for single images or batch processing of a directory.

GWDTMultiSomaFileCmd() - Constructor for class sc.fiji.snt.plugin.GWDTMultiSomaFileCmd

GWDTTracer<T> - Class in sc.fiji.snt.tracing.auto

In-memory GWDT tracer using array storage.

GWDTTracer(ImagePlus) - Constructor for class sc.fiji.snt.tracing.auto.GWDTTracer

Creates a new GWDTTracer from an ImagePlus.

GWDTTracer(ImgPlus<T>) - Constructor for class sc.fiji.snt.tracing.auto.GWDTTracer

Creates a new GWDTTracer from an ImgPlus.

GWDTTracer(RandomAccessibleInterval<T>) - Constructor for class sc.fiji.snt.tracing.auto.GWDTTracer

Creates a new GWDTTracer with isotropic spacing (1.0 for each dimension).

GWDTTracer(RandomAccessibleInterval<T>, double[]) - Constructor for class sc.fiji.snt.tracing.auto.GWDTTracer

Creates a new GWDTTracer.

GWDTTracerCmd - Class in sc.fiji.snt.plugin

Interactive command providing a GUI for GWDT autotracing when an image is already loaded in SNT.

GWDTTracerCmd() - Constructor for class sc.fiji.snt.plugin.GWDTTracerCmd

GWDTTracerCommonCmd - Class in sc.fiji.snt.plugin

Base command providing shared parameters and logic for GWDT autotracing.

GWDTTracerCommonCmd() - Constructor for class sc.fiji.snt.plugin.GWDTTracerCommonCmd

GWDTTracerFactory - Class in sc.fiji.snt.tracing.auto

Factory for creating optimal GWDT tracer implementations based on image size.

GWDTTracerFactory() - Constructor for class sc.fiji.snt.tracing.auto.GWDTTracerFactory

GWDTTracerFileCmd - Class in sc.fiji.snt.plugin

Non-interactive command for file-based GWDT autotracing with support for single images or batch processing of an entire directory.

GWDTTracerFileCmd() - Constructor for class sc.fiji.snt.plugin.GWDTTracerFileCmd

H

h - Variable in class sc.fiji.snt.tracing.DefaultSearchNode

HAND - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

handleTracedTrees(List<Tree>) - Method in class sc.fiji.snt.plugin.AutotraceFromBinaryTipsCmd

Intercepts the trees produced by the parent's binary-tracer flow, prunes each one to keep only the paths on a root-to-tip route, and forwards the pruned result to the parent's standard tree-handling (which adds them to the Path Manager, optionally with proofreading and color assignment, per the "After tracing" choice).

handleTracedTrees(List<Tree>) - Method in class sc.fiji.snt.plugin.BinaryTracerCmd

handleTracedTrees(List<Tree>) - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

Called after tracing completes with valid trees.

handleTracedTrees(List<Tree>) - Method in class sc.fiji.snt.plugin.BinaryTracerFileCmd

handleTracedTrees(List<Tree>) - Method in class sc.fiji.snt.plugin.GWDTMultiSomaFileCmd

handleTracedTrees(List<Tree>) - Method in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

Called after tracing completes with valid trees.

handleTracedTrees(List<Tree>) - Method in class sc.fiji.snt.plugin.GWDTTracerFileCmd

hasBookmarks() - Method in class sc.fiji.snt.BookmarkManager

Returns whether any bookmarks exist.

hasColor() - Method in class sc.fiji.snt.Path.PathNode

hasContext() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollTable

hasContour() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Checks if a valid contour was extracted.

hasCustomColor() - Method in class sc.fiji.snt.Path

Assesses whether a custom color has been assigned to this Path.

hasDelineationLabels(Collection<Tree>) - Static method in class sc.fiji.snt.DelineationsManager

Checks if the given trees have any delineation labels.

hasDelineationLabels(Tree) - Static method in class sc.fiji.snt.DelineationsManager

Checks if the given tree has any delineation labels.

hasDimensions() - Method in class sc.fiji.snt.util.BoundingBox

hasElongationEvents() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Checks if this neurite has elongation events.

hasExtraMeasurement() - Method in class sc.fiji.snt.analysis.sholl.Profile

hashCode() - Method in record class sc.fiji.snt.analysis.CircularModels.VonMisesFit

Returns a hash code value for this object.

hashCode() - Method in record class sc.fiji.snt.analysis.curation.CurationTags.Partition

Returns a hash code value for this object.

hashCode() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCalibrator.CheckSummary

Returns a hash code value for this object.

hashCode() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCheck.Warning

Returns a hash code value for this object.

hashCode() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalysisResults.GrowthSummaryStatistics

Returns a hash code value for this object.

hashCode() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.ElongationEvent

Returns a hash code value for this object.

hashCode() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhase

Returns a hash code value for this object.

hashCode() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.RetractionEvent

Returns a hash code value for this object.

hashCode() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.TimePoint

Returns a hash code value for this object.

hashCode() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

hashCode() - Method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Returns a hash code value for this object.

hashCode() - Method in record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.PolarPeak

Returns a hash code value for this object.

hashCode() - Method in record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.Report

Returns a hash code value for this object.

hashCode() - Method in class sc.fiji.snt.analysis.sholl.Profile

hashCode() - Method in class sc.fiji.snt.annotation.AllenCompartment

hashCode() - Method in class sc.fiji.snt.annotation.DrosophilaCompartment

hashCode() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

hashCode() - Method in record class sc.fiji.snt.io.OmeAxisUtils.OmeMetadata

Returns a hash code value for this object.

hashCode() - Method in record class sc.fiji.snt.MultiPathTracerCanvas.Entry

Returns a hash code value for this object.

hashCode() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Returns a hash code value for this object.

hashCode() - Method in class sc.fiji.snt.tracing.BiSearchNode

hashCode() - Method in class sc.fiji.snt.tracing.DefaultSearchNode

hashCode() - Method in class sc.fiji.snt.util.BoundingBox

hashCode() - Method in record class sc.fiji.snt.util.ImgUtils.SliceResult

Returns a hash code value for this object.

hashCode() - Method in class sc.fiji.snt.util.PointInImage

hashCode() - Method in class sc.fiji.snt.util.SNTColor

hashCode() - Method in class sc.fiji.snt.util.SWCPoint

hashCode() - Method in record class sc.fiji.snt.util.TreeUtils.EndpointClusterAnalysis

Returns a hash code value for this object.

hashCode() - Method in record class sc.fiji.snt.util.TreeUtils.EndpointMatch

Returns a hash code value for this object.

hashCode() - Method in class sc.fiji.snt.viewer.Viewer3D

hasImage() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.SignalQuality

hasNext - Variable in class sc.fiji.snt.util.CircleCursor3D

hasNext() - Method in class sc.fiji.snt.PathAndFillManager.AllPointsIterator

hasNext() - Method in class sc.fiji.snt.util.CircleCursor3D

hasNext() - Method in class sc.fiji.snt.util.DiskCursor3D

hasNext() - Method in class sc.fiji.snt.util.PathCursor

hasNodeAnnotations() - Method in class sc.fiji.snt.Path

Assesses whether the nodes of this path have been assigned BrainAnnotations.

hasNodeColors() - Method in class sc.fiji.snt.Path

Checks whether any nodes have custom colors assigned.

hasNodeHemisphereFlags() - Method in class sc.fiji.snt.Path

Assesses whether the nodes of this path have been assigned hemisphere flags.

hasNodeValues() - Method in class sc.fiji.snt.Path

Assesses whether the nodes of this path have been assigned an array of values

hasPhaseType(GrowthAnalyzer.GrowthPhaseType) - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Checks if this neurite has any phases of the specified type.

hasPoints() - Method in class sc.fiji.snt.analysis.sholl.Profile

hasRadii() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCalibrator.CalibrationResult

hasRadii() - Method in class sc.fiji.snt.Path

Checks whether the nodes of this path have been assigned defined thickness.

hasRadius() - Method in class sc.fiji.snt.Path.PathNode

hasRapidGrowth() - Static method in interface sc.fiji.snt.analysis.growth.GrowthAnalysisResults.NeuriteSelectionCriterion

hasReconstructions() - Method in class sc.fiji.snt.io.InsectBrainLoader.NeuronInfo

hasRetractionEvents() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Checks if this neurite has retraction events.

hasRetractions() - Static method in interface sc.fiji.snt.analysis.growth.GrowthAnalysisResults.NeuriteSelectionCriterion

hasSpacingUnits() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Returns true if spacing units are defined.

hasTangent() - Method in class sc.fiji.snt.Path.PathNode

hasTangents() - Method in class sc.fiji.snt.Path

Checks whether any nodes have tangent vectors defined.

hasUnsavedData() - Method in class sc.fiji.snt.analysis.SNTTable

Checks if the table has unsaved data.

haveSameSpatialDimensions(ImagePlus, RandomAccessibleInterval<?>) - Static method in class sc.fiji.snt.util.ImgUtils

Checks whether an ImagePlus and a RandomAccessibleInterval have compatible spatial dimensions (width, height, and optionally depth).

haveSameSpatialDimensions(RandomAccessibleInterval<?>, RandomAccessibleInterval<?>) - Static method in class sc.fiji.snt.util.ImgUtils

Checks whether two images have compatible spatial dimensions (width, height, and optionally depth).

HEADER_HTML - Static variable in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

HEADER_HTML - Static variable in class sc.fiji.snt.plugin.ShollAnalysisImgCommonCmd

HEADER_HTML - Static variable in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

HEADER_TOOLTIP - Static variable in class sc.fiji.snt.plugin.ShollAnalysisImgCommonCmd

headless - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

heapDecreaseKey(boolean) - Method in class sc.fiji.snt.tracing.BiSearchNode

heapHandle - Variable in class sc.fiji.snt.tracing.DefaultSearchNode

heapInsert(AddressableHeap<BiSearchNode, Void>, boolean) - Method in class sc.fiji.snt.tracing.BiSearchNode

HEART_CIRCLE_BOLT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

HEART_PULSE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

HEAVY_PATH_DECOMPOSITION - Static variable in class sc.fiji.snt.analysis.graph.GraphColorMapper

Flag for "Heavy path decomposition" mapping.

height - Variable in class sc.fiji.snt.SNT

height() - Method in class sc.fiji.snt.util.BoundingBox

HEIGHT - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Height"

help(String) - Static method in class sc.fiji.snt.gui.GuiUtils.Buttons

helpMenu(SNTCommandFinder) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

HEMI_EAST - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

HEMI_NONE - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

HEMI_NORTH - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

HEMI_SOUTH - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

HEMI_WEST - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

HERMIT - Static variable in class sc.fiji.snt.PathNodeCanvas

Flag describing a single point path

HessianGenerationCallback - Interface in sc.fiji.snt

Represents a callback interface for monitoring the progress of Hessian filtering.

heuristic - Variable in class sc.fiji.snt.tracing.BiSearch

Heuristic - Interface in sc.fiji.snt.tracing.heuristic

Interface for heuristic estimates to the goal used by classes implementing SearchInterface.

hierarchicalPrune(DirectedWeightedGraph, double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Performs hierarchical pruning using intensity-weighted coverage.

HIGHEST_PATH_ORDER - Static variable in class sc.fiji.snt.analysis.MultiTreeColorMapper

Mapping property: Highest path order

HIGHEST_PATH_ORDER - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics

Flag specifying "Highest path order" statistics

highGrowthRate(double) - Static method in interface sc.fiji.snt.analysis.growth.GrowthAnalysisResults.NeuriteSelectionCriterion

highlighted() - Method in record class sc.fiji.snt.MultiPathTracerCanvas.Entry

Returns the value of the highlighted record component.

HOME - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

honoredSeedRoles() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

GWDT tracers consume AutoTracer.SeedRole.ROOT (the Fast-Marching source voxel), AutoTracer.SeedRole.TIP (target endpoints reachable from the root via parent pointers), and AutoTracer.SeedRole.WAYPOINT (soft path attractors implemented by biasing the GWDT cost map before Fast Marching).

honoredSeedRoles() - Method in interface sc.fiji.snt.tracing.auto.AutoTracer

honoredSeedRoles() - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Binary tracers currently consume only the AutoTracer.SeedRole.ROOT role.

hostedMeshesLocation() - Static method in class sc.fiji.snt.annotation.AllenUtils

HYPERSPHERE - Enum constant in enum class sc.fiji.snt.analysis.ProfileProcessor.Shape

I

ICE - Static variable in class sc.fiji.snt.util.ColorMaps

iconColor() - Static method in class sc.fiji.snt.gui.SearchField

IconFactory - Class in sc.fiji.snt.gui

A factory for FADerivedIcons presets.

IconFactory() - Constructor for class sc.fiji.snt.gui.IconFactory

IconFactory.GLYPH - Enum Class in sc.fiji.snt.gui

iconHeaderRenderer(Icon, String) - Static method in class sc.fiji.snt.gui.GuiUtils.JTables

Creates a header renderer that displays a centered icon instead of text.

id - Variable in class sc.fiji.snt.util.SWCPoint

The sample number of this node

id() - Method in class sc.fiji.snt.annotation.AllenCompartment

id() - Method in interface sc.fiji.snt.annotation.BrainAnnotation

Returns the compartment's unique id.

id() - Method in class sc.fiji.snt.annotation.DrosophilaCompartment

id() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

ID - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

ID - Static variable in class sc.fiji.snt.analysis.MultiTreeColorMapper

Mapping property (dummy): Each Tree in the collection is assigned an incremental LUT entry

ID_ALT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

identifier() - Method in class sc.fiji.snt.analysis.sholl.Profile

idExists() - Method in class sc.fiji.snt.io.InsectBrainLoader

Checks whether the neuron to be loaded was found in the database.

idExists() - Method in class sc.fiji.snt.io.MouseLightLoader

Checks if the neuron ID exists in the database.

IGNORED_CMD - Static variable in class sc.fiji.snt.gui.ScriptRecorder

IMAGE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

ImageParser - Class in sc.fiji.snt.analysis.sholl.parsers

A Parser for extracting Sholl profiles from image data.

ImageParser(ImagePlus) - Constructor for class sc.fiji.snt.analysis.sholl.parsers.ImageParser

Deprecated.

ImageParser(ImagePlus, Context) - Constructor for class sc.fiji.snt.analysis.sholl.parsers.ImageParser

ImageParser2D - Class in sc.fiji.snt.analysis.sholl.parsers

Sholl Parser for 2D images

ImageParser2D(ImagePlus) - Constructor for class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D

ImageParser2D(ImagePlus, Context) - Constructor for class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D

ImageParser3D - Class in sc.fiji.snt.analysis.sholl.parsers

Parser for 3D images

ImageParser3D(ImagePlus) - Constructor for class sc.fiji.snt.analysis.sholl.parsers.ImageParser3D

ImageParser3D(ImagePlus, Context) - Constructor for class sc.fiji.snt.analysis.sholl.parsers.ImageParser3D

imageType - Variable in class sc.fiji.snt.SNT

imageTypeToString(int) - Static method in class sc.fiji.snt.util.ImpUtils

img - Variable in class sc.fiji.snt.tracing.AbstractSearch

img() - Method in record class sc.fiji.snt.util.ImgUtils.SliceResult

Returns the value of the img record component.

imgAccess - Variable in class sc.fiji.snt.tracing.AbstractSearch

imgChoice - Variable in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

imgDepth - Variable in class sc.fiji.snt.tracing.AbstractSearch

The depth (number of slices) of the search image.

imgFileChoice - Variable in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

imgHeight - Variable in class sc.fiji.snt.tracing.AbstractSearch

The height of the search image in pixels.

imgPlusToCalibration(ImgPlus<?>) - Static method in class sc.fiji.snt.util.ImgUtils

Deprecated.

Use ImgUtils.getCalibration(ImgPlus) instead

ImgUtils - Class in sc.fiji.snt.util

Static utilities for handling and manipulation of RandomAccessibleIntervals

ImgUtils.SliceResult<T> - Record Class in sc.fiji.snt.util

Result of a channel/time slice extraction from an ImgPlus.

imgWidth - Variable in class sc.fiji.snt.tracing.AbstractSearch

The width of the search image in pixels.

imp - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

impMap - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

IMPORT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

importFromLabelImage(ImagePlus) - Method in class sc.fiji.snt.DelineationsManager

Convenience overload accepting an ImagePlus, which is converted to an ImgPlus via ImpUtils.toImgPlus3D(ImagePlus, int, int).

importFromLabelImage(RandomAccessibleInterval<? extends RealType<?>>) - Method in class sc.fiji.snt.DelineationsManager

Imports delineations from a labels image.

importFromLabelImage(RandomAccessibleInterval<? extends RealType<?>>, double[]) - Method in class sc.fiji.snt.DelineationsManager

Imports delineations from a labels image with explicit pixel spacing.

importGraph(DirectedWeightedGraph) - Method in class sc.fiji.snt.PathAndFillManager

importGraphWithPathStructure(DirectedWeightedGraph) - Method in class sc.fiji.snt.PathAndFillManager

importNeurons(Map<String, TreeSet<SWCPoint>>, ColorRGB, String) - Method in class sc.fiji.snt.PathAndFillManager

Import neuron(s) as a collection of reconstruction nodes (SWC points)

ImportSeedPointsCmd - Class in sc.fiji.snt.gui.cmds

Imports candidate seed points from a CSV file into SNT's SeedOverlay.

ImportSeedPointsCmd() - Constructor for class sc.fiji.snt.gui.cmds.ImportSeedPointsCmd

importSWC(BufferedReader, String, boolean, double, double, double, double, double, double, double, boolean, int...) - Method in class sc.fiji.snt.PathAndFillManager

Imports SWC data with advanced settings.

importSWC(String, boolean) - Method in class sc.fiji.snt.PathAndFillManager

Imports an SWC file.

importSWC(String, boolean, double, double, double, double, double, double, double, boolean, int...) - Method in class sc.fiji.snt.PathAndFillManager

Imports an SWC file using advanced options.

importSWC(String, String) - Method in class sc.fiji.snt.PathAndFillManager

Imports an SWC file using default settings.

importSWCs(Map<String, String>, ColorRGB) - Method in class sc.fiji.snt.PathAndFillManager

Imports a group of SWC files (Remote URLs supported).

improveRecording() - Static method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

Customizes macro recordings

impToRealRai5d(ImagePlus) - Static method in class sc.fiji.snt.util.ImgUtils

Wrap an ImagePlus to a RandomAccessibleInterval such that the number of dimensions in the resulting rai is 5 and the axis order is XYCZT.

ImpUtils - Class in sc.fiji.snt.util

Static utilities for handling and manipulation of ImagePluss

IN_DEGREE - Static variable in class sc.fiji.snt.analysis.graph.GraphColorMapper

Flag for "In degree" mapping.

includeDirectChildren(boolean) - Method in class sc.fiji.snt.util.CrossoverFinder.Config

Sets CrossoverFinder.Config.includeDirectChildren.

includes(BrainAnnotation) - Method in class sc.fiji.snt.annotation.AllenCompartment

includeSelfCrossovers(boolean) - Method in class sc.fiji.snt.util.CrossoverFinder.Config

Sets CrossoverFinder.Config.includeSelfCrossovers.

INCOMING_WEIGHT - Static variable in class sc.fiji.snt.analysis.graph.GraphColorMapper

Flag for "Incoming weight" mapping.

INDEX - Enum constant in enum class sc.fiji.snt.seed.SeedOverlay.ColorMode

indexInPath - Variable in class sc.fiji.snt.NearPoint

The index of this point within its associated path

indexNearestTo(double, double, double) - Method in class sc.fiji.snt.Path

indexNearestTo(double, double, double, double) - Method in class sc.fiji.snt.Path

Gets the index of the closest node associated with the specified world coordinates.

indexNearestToCanvasPosition2D(double, double, double) - Method in class sc.fiji.snt.Path

indexNearestToUnscaled(double, double, double) - Method in class sc.fiji.snt.Path

Returns the index of the node nearest to the specified position in pixel (unscaled) coordinates, searching across all nodes regardless of distance.

indexNearestToUnscaled(double, double, double, double) - Method in class sc.fiji.snt.Path

Returns the index of the node nearest to the specified position in pixel (unscaled) coordinates.

indexOf(Path) - Method in class sc.fiji.snt.Tree

Returns the index of the specified Path in this Tree.

indexOf(SeedPoint) - Method in class sc.fiji.snt.seed.SeedOverlay

Returns the index of seed in the data list, or -1 if absent.

indexToPos(long, long[]) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Convert linear index to position, writing to provided array (avoids allocation).

indexWindow - Variable in class sc.fiji.snt.util.CrossoverFinder.CrossoverEvent

Min/max of node indices per path near the event

inferSpacing(Collection<SWCPoint>) - Method in class sc.fiji.snt.util.BoundingBox

Infers the voxel spacing of this box from the inter-node distances of a Collection of SWCPoints.

info - Variable in class sc.fiji.snt.util.BoundingBox

Used to store information about this bounding box.

info(Object) - Method in class sc.fiji.snt.util.Logger

Logs an informational message.

info(String) - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

Displays an informational message via the SNT UI, or logs it if no UI is available.

INFO - Enum constant in enum class sc.fiji.snt.analysis.curation.PlausibilityCheck.Severity

Informational: the operation is unusual but not necessarily wrong.

INFO - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

infoColor() - Static method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

init() - Method in class sc.fiji.snt.gui.cmds.BvvRenderingOptionsCmd

init() - Method in class sc.fiji.snt.gui.cmds.ChooseDatasetCmd

init() - Method in class sc.fiji.snt.gui.cmds.ColorMapReconstructionCmd

init() - Method in class sc.fiji.snt.gui.cmds.ComputeSecondaryImg

init() - Method in class sc.fiji.snt.gui.cmds.CostFunctionSelectionCmd

init() - Method in class sc.fiji.snt.gui.cmds.DistributionBPCmd

init() - Method in class sc.fiji.snt.gui.cmds.DistributionCPCmd

init() - Method in class sc.fiji.snt.gui.cmds.GraphGeneratorCmd

init() - Method in class sc.fiji.snt.gui.cmds.InsectBrainImporterCmd

init() - Method in class sc.fiji.snt.gui.cmds.LoadReconstructionCmd

init() - Method in class sc.fiji.snt.gui.cmds.LoadSeedsFromLabelsImageCmd

init() - Method in class sc.fiji.snt.gui.cmds.MLImporterCmd

init() - Method in class sc.fiji.snt.gui.cmds.RemoteSWCImporterCmd

init() - Method in class sc.fiji.snt.gui.cmds.TranslateReconstructionsCmd

init() - Method in class sc.fiji.snt.gui.cmds.TwoDHistCmd

init() - Method in class sc.fiji.snt.plugin.AutotraceFromBinarySeedsCmd

Initializer.

init() - Method in class sc.fiji.snt.plugin.AutotraceFromBinaryTipsCmd

Initializer.

init() - Method in class sc.fiji.snt.plugin.AutotraceFromSeedsCmd

Initializer.

init() - Method in class sc.fiji.snt.plugin.AutotraceFromTipsCmd

Initializer.

init() - Method in class sc.fiji.snt.plugin.AutotraceFromWaypointsCmd

Initializer.

init() - Method in class sc.fiji.snt.plugin.ChooseDataset

init() - Method in class sc.fiji.snt.plugin.PlotterCmd

init() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCmd

init() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCommonCmd

init() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgInteractiveCmd

init() - Method in class sc.fiji.snt.plugin.ShollAnalysisTreeCmd

init(boolean) - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

init(Collection<SWCPoint>, boolean) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

initForFile() - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

Initializes the command for file-based (batch) mode.

initForFile() - Method in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

initForImage() - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

Initializes the command for interactive (image-choice) mode.

initForImage() - Method in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

initialize() - Method in class sc.fiji.snt.gui.cmds.SNTLoaderCmd

initialize(boolean) - Method in class sc.fiji.snt.SNTService

Initializes SNT.

initialize(boolean, int, int) - Method in class sc.fiji.snt.SNT

Initializes the plugin by assembling all the required tracing views

initialize(boolean, int, int, boolean) - Method in class sc.fiji.snt.SNT

initialize(ImagePlus) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

initialize(ImagePlus) - Method in class sc.fiji.snt.SNT

initialize(ImagePlus, boolean) - Method in class sc.fiji.snt.SNTService

Initializes SNT.

initialize(ImagePlus, int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

initialize(String, boolean) - Method in class sc.fiji.snt.SNTService

Initializes SNT.

initialize(ImgPlus<T>, boolean) - Method in class sc.fiji.snt.SNTService

Initializes SNT from an ImgPlus image.

initializeFastMarching(long[], long) - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

initializeFastMarching(long[], long) - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

initializeFastMarching(long[], long) - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

initializeFastMarching(long[], long) - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Initialize Fast Marching data structures.

initLookAndFeel() - Method in class sc.fiji.snt.gui.cmds.PrefsCmd

initLuts() - Method in class sc.fiji.snt.analysis.ColorMapper

initMultiSoma() - Method in class sc.fiji.snt.plugin.GWDTMultiSomaCommonCmd

Initializes multi-soma commands by hiding the single-cell soma/ROI parameters inherited from the parent.

initPathsToFill(Set<Path>, boolean) - Method in class sc.fiji.snt.SNT

initSplashScreen() - Static method in class sc.fiji.snt.gui.GuiUtils

INNER_EXTENSION_ANGLE - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying Inner branches: Extension angle

INNER_EXTENSION_ANGLE_REL - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying Inner branches: Extension angle (Rel.)

INNER_EXTENSION_ANGLE_XY - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Inner branches: Extension angle XY"

INNER_EXTENSION_ANGLE_XZ - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Inner branches: Extension angle XZ"

INNER_EXTENSION_ANGLE_ZY - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Inner branches: Extension angle ZY"

INNER_LENGTH - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics

Flag for "Length of inner branches (sum)" analysis.

INNER_LENGTH - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Inner branches: Length"

innerBranches - Variable in class sc.fiji.snt.analysis.TreeStatistics

innerRadius(double) - Method in class sc.fiji.snt.analysis.detection.PeripathDetector.Config

innerRadiusMultiplier(double) - Method in class sc.fiji.snt.analysis.detection.PeripathDetector.Config

inputCounts - Variable in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

inputCounts - Variable in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

inputDir - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

inputImageChanged() - Method in class sc.fiji.snt.SNTUI

inputRadii - Variable in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

inputRadii - Variable in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

InsectBrainCompartment - Class in sc.fiji.snt.annotation

InsectBrainCompartment() - Constructor for class sc.fiji.snt.annotation.InsectBrainCompartment

InsectBrainImporterCmd - Class in sc.fiji.snt.gui.cmds

Command for importing InsectBrain reconstructions

InsectBrainImporterCmd() - Constructor for class sc.fiji.snt.gui.cmds.InsectBrainImporterCmd

InsectBrainLoader - Class in sc.fiji.snt.io

Methods for retrieving reconstructions and annotations from the Insect Brain Database at insectbraindb.org *

InsectBrainLoader(int) - Constructor for class sc.fiji.snt.io.InsectBrainLoader

Constructs a new InsectBrainLoader for the specified neuron ID.

InsectBrainLoader.NeuronInfo - Class in sc.fiji.snt.io

InsectBrainUtils - Class in sc.fiji.snt.annotation

Utility methods for retrieving species, brain, and neuron data from the Insect Brain Database

insertNode(int, PointInImage) - Method in class sc.fiji.snt.Path

Inserts a node at a specified position.

insertNode(int, SNTPoint) - Method in class sc.fiji.snt.Path

Inserts a node at the specified position.

insertRow(String) - Method in class sc.fiji.snt.analysis.SNTTable

install(TracerCanvas, SNT) - Static method in class sc.fiji.snt.seed.SeedOverlayCanvasHandler

Installs the Alt+Click → edit-nearest-seed listener on the given canvas.

installComponents() - Method in class sc.fiji.snt.gui.SNTSearchableBar

installHandlers() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

installListeners() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

installMenuItem(JPopupMenu) - Method in class sc.fiji.snt.gui.GuiUtils.JTables.DetachableTable

Adds a "Detach Table" / "Dock Table" toggle item to the given popup menu.

integerScale - Variable in class sc.fiji.snt.analysis.ColorMapper

integerSpinner(int, int, int, int, boolean) - Static method in class sc.fiji.snt.gui.GuiUtils

intensity - Variable in class sc.fiji.snt.analysis.detection.Detection

Intensity at the detection site

INTENSITY_WEIGHT_KEY - Static variable in class sc.fiji.snt.gui.cmds.MultiSpectralRefinerCmd

intensityWeight() - Method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Returns the value of the intensityWeight record component.

INTER_NODE_ANGLE - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Internode angle

INTER_NODE_ANGLE - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Internode angle"

INTER_NODE_DISTANCE - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Internode distance

INTER_NODE_DISTANCE - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Internode distance"

INTER_NODE_DISTANCE_SQUARED - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Internode distance (squared)"

interpolateMissingRadii(DoublePredicate, boolean) - Method in class sc.fiji.snt.Path

Deprecated.

Use Path.sanitizeRadii(DoublePredicate, boolean) instead

interpolateNullEntries(Color[]) - Static method in class sc.fiji.snt.util.SNTColor

Replaces null colors in an array with the average of flanking non-null colors.

InterpolateRadiiCmd - Class in sc.fiji.snt.plugin

Command for finding all the nodes in a collection of paths with invalid radius, and assign them interpolated values from their neighbors and Viewer3D

InterpolateRadiiCmd() - Constructor for class sc.fiji.snt.plugin.InterpolateRadiiCmd

interpolateRadius(double[], int, double) - Static method in class sc.fiji.snt.analysis.detection.DetectorUtils

Simple linear interpolation for a missing radius value at idx, using the nearest valid neighbors.

intersection(Collection<AnnotationGraph>) - Static method in class sc.fiji.snt.analysis.graph.AnnotationGraphUtils

Return the graph representing the intersection of the edge sets of a collection of graphs.

intersection(AbstractConvexHull...) - Method in class sc.fiji.snt.analysis.AbstractConvexHull

Returns the intersection of this convex hull with the given hull(s).

intersection(AbstractConvexHull...) - Method in class sc.fiji.snt.analysis.ConvexHull2D

intersection(AbstractConvexHull...) - Method in class sc.fiji.snt.analysis.ConvexHull3D

intersection(BoundingBox) - Method in class sc.fiji.snt.util.BoundingBox

Retrieves the intersection cuboid between this bounding with another bounding box.

intersectionBox(AbstractConvexHull...) - Method in class sc.fiji.snt.analysis.AbstractConvexHull

Returns the bounding-box intersection of this hull with the given hull(s).

INTERSECTIONS - Enum constant in enum class sc.fiji.snt.analysis.sholl.math.ShollStats.DataMode

INTG_MEAN - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

INTG_MEDIAN - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

INTG_MODE - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

invalidStatsError(boolean) - Method in class sc.fiji.snt.SNT

invertLut(ImagePlus) - Static method in class sc.fiji.snt.util.ImpUtils

is2D() - Method in class sc.fiji.snt.analysis.sholl.Profile

is2D() - Method in class sc.fiji.snt.SNT

is2DDisplayCanvas() - Method in class sc.fiji.snt.SNTPrefs

Checks if 2D display canvas is forced.

is2Dnormalization() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

is3D() - Method in class sc.fiji.snt.Tree

Assesses whether this Tree has depth.

is3Dnormalization() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

isActive() - Method in class sc.fiji.snt.SNTService

Gets whether SNT is running.

isActive() - Method in class sc.fiji.snt.viewer.Viewer3D

Checks whether this instance is currently active

isActiveVersion() - Method in class sc.fiji.snt.Path

Checks if this version of the path is currently being used for display/analysis.

isAllowVoxelGap() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Returns whether gap bridging is enabled (single- or multi-voxel).

isAncestorOf(Path, Path) - Static method in class sc.fiji.snt.util.TreeUtils

Checks if 'potentialAncestor' is an ancestor of 'potentialDescendant'.

isAnnotated() - Method in class sc.fiji.snt.Tree

Checks if the nodes of this Tree have been assigned BrainAnnotations (neuropil labels).

isAssumePixelCoordinates() - Method in class sc.fiji.snt.gui.SWCImportDialog

isAstarEnabled() - Method in class sc.fiji.snt.SNT

Checks if A* search is enabled

isAutoDetectAnimationAxis() - Method in class sc.fiji.snt.viewer.Viewer3D

Returns whether automatic rotation axis detection is enabled.

isAutoFilter() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Returns whether automatic soma filtering is enabled.

isAutoLayout() - Method in class sc.fiji.snt.gui.ComponentMover

Get the auto layout property

isBeingEdited() - Method in class sc.fiji.snt.Path

isBinary(ImagePlus) - Static method in class sc.fiji.snt.util.ImpUtils

isBinary(RandomAccessibleInterval<?>) - Static method in class sc.fiji.snt.util.ImgUtils

isBinaryMask(ImagePlus) - Static method in class sc.fiji.snt.seed.LabelsToSeeds

Detects whether imp is a binary mask, i.e. all non-zero voxels share a single value.

isBranchesAssigned() - Method in class sc.fiji.snt.analysis.NodeStatistics

isCachedData(ImagePlus) - Method in class sc.fiji.snt.SNT

isCalibrationCompatible(ImagePlus) - Method in class sc.fiji.snt.gui.cmds.ChooseDatasetCmd

isCanceled() - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

isCellEditable(int, int) - Method in class sc.fiji.snt.seed.SeedTableModel

All cells are read-only.

isChangeCursor() - Method in class sc.fiji.snt.gui.ComponentMover

Get the change cursor property

isChildOf(BrainAnnotation) - Method in class sc.fiji.snt.annotation.AllenCompartment

Assesses if this annotation is a child of a specified compartment.

isChildOf(BrainAnnotation) - Method in interface sc.fiji.snt.annotation.BrainAnnotation

Returns whether this compartment is a sub-compartment of annotation.

isChildOf(BrainAnnotation) - Method in class sc.fiji.snt.annotation.DrosophilaCompartment

isChildOf(BrainAnnotation) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

isClipAnnotationsToSlab() - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Returns true if annotation/marker rendering is restricted to the slab Z range.

isClipPathsToSlab() - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Returns true if path rendering is restricted to the slab Z range.

isClippingEnabled() - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Gets whether 'clipped visibility' is enabled

isCollapsed() - Method in class sc.fiji.snt.gui.CollapsiblePanel

Checks if this panel is currently collapsed.

isColorCodeAllowed() - Method in class sc.fiji.snt.viewer.Annotation3D

isColorPairingEnabled() - Method in class sc.fiji.snt.gui.cmds.SWCTypeOptionsCmd

isCombined() - Method in class sc.fiji.snt.analysis.SNTChart

Checks if this chart is part of a multi-panel montage

isConnectedTo(Path) - Method in class sc.fiji.snt.Path

isContextSet() - Static method in class sc.fiji.snt.SNTUtils

isDarkModeOn() - Method in class sc.fiji.snt.viewer.Viewer3D

Checks if scene is being rendered under dark or light background.

isDatabaseAvailable() - Static method in class sc.fiji.snt.annotation.VFBUtils

Checks whether a connection to the Virtual Fly Brain database can be established.

isDatabaseAvailable() - Static method in class sc.fiji.snt.annotation.ZBAtlasUtils

Checks whether a connection to the FishAtlas database can be established.

isDatabaseAvailable() - Method in class sc.fiji.snt.io.FlyCircuitLoader

Checks whether a connection to the FlyCircuit database can be established.

isDatabaseAvailable() - Static method in class sc.fiji.snt.io.InsectBrainLoader

Checks whether a connection to the Insect Brain Database can be established.

isDatabaseAvailable() - Static method in class sc.fiji.snt.io.MouseLightLoader

Checks whether a connection to the MouseLight database can be established.

isDatabaseAvailable() - Static method in class sc.fiji.snt.io.MouseLightQuerier

Checks whether a connection to the MouseLight database can be established.

isDatabaseAvailable() - Method in class sc.fiji.snt.io.NeuroMorphoLoader

Checks whether a connection to the NeuroMorpho database can be established.

isDatabaseAvailable() - Method in interface sc.fiji.snt.io.RemoteSWCLoader

isDebug() - Method in class sc.fiji.snt.util.Logger

Checks if debug mode is enabled.

isDebugMode() - Static method in class sc.fiji.snt.SNTUtils

Assesses if SNT is running in debug mode

isDescendantOf(Path, Path) - Static method in class sc.fiji.snt.util.TreeUtils

Checks if 'potentialDescendant' is a descendant of 'potentialAncestor'.

isDetached() - Method in class sc.fiji.snt.gui.GuiUtils.JTables.DetachableTable

isDetailsView() - Method in class sc.fiji.snt.gui.FileChooser

Checks if the current view type is details view.

isDisplayCanvas(ImagePlus) - Method in class sc.fiji.snt.SNT

isDisplayRadii() - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Returns whether paths are rendered as tapered frustums (true) or simple lines (false).

isDummy() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

isEdgeLabelsEnabled() - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter

isEditable() - Method in class sc.fiji.snt.PathNodeCanvas

isEditableNodeLocked() - Method in class sc.fiji.snt.Path

isEditingFittedPath() - Method in class sc.fiji.snt.SNT

Returns whether the path currently being edited is displayed as its fitted version.

isEditModeEnabled() - Method in class sc.fiji.snt.SNT

isEmpty() - Method in class sc.fiji.snt.analysis.sholl.Profile

isEmpty() - Method in class sc.fiji.snt.seed.SeedOverlay

isEmpty() - Method in class sc.fiji.snt.Tree

Checks if this Tree is empty.

isEnabled() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.DeepCheck

isEnabled() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.LiveCheck

isEnabled() - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

isEnabled() - Method in class sc.fiji.snt.gui.CheckboxSpinner

isEqualized() - Method in class sc.fiji.snt.analysis.SNTChart

Checks if the axes of the underlying XY plot are equalized.

isEventsDisabled() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

isExactMetricMatch() - Static method in class sc.fiji.snt.analysis.TreeStatistics

Checks if 'fuzzy matching' of metrics is active.

isFileMode() - Method in class sc.fiji.snt.plugin.AutotraceFromBinarySeedsCmd

isFileMode() - Method in class sc.fiji.snt.plugin.AutotraceFromBinaryTipsCmd

isFileMode() - Method in class sc.fiji.snt.plugin.AutotraceFromSeedsCmd

isFileMode() - Method in class sc.fiji.snt.plugin.AutotraceFromTipsCmd

isFileMode() - Method in class sc.fiji.snt.plugin.AutotraceFromWaypointsCmd

isFileMode() - Method in class sc.fiji.snt.plugin.BinaryTracerCmd

isFileMode() - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

Returns whether this command operates in file mode (loading images from file paths) or in image-choice mode (selecting from open images).

isFileMode() - Method in class sc.fiji.snt.plugin.BinaryTracerFileCmd

isFileMode() - Method in class sc.fiji.snt.plugin.GWDTMultiSomaCmd

isFileMode() - Method in class sc.fiji.snt.plugin.GWDTMultiSomaFileCmd

isFileMode() - Method in class sc.fiji.snt.plugin.GWDTTracerCmd

isFileMode() - Method in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

isFileMode() - Method in class sc.fiji.snt.plugin.GWDTTracerFileCmd

isFittedVersionOfAnotherPath() - Method in class sc.fiji.snt.Path

Checks if this Path is a fitted version of another path.

isGMMDistributionVisible() - Method in class sc.fiji.snt.analysis.SNTChart

Gets whether the GMM distribution curve is being overlaid over histogram frequencies

isGridlinesVisible() - Method in class sc.fiji.snt.analysis.SNTChart

isHeadless() - Static method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

isInBounds(long[]) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Checks if a voxel position is within image bounds.

isInsideSomaRoi(SWCPoint) - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Checks if a point is inside the soma ROI.

isInSubtree(Path, Path) - Static method in class sc.fiji.snt.util.TreeUtils

Checks if 'target' is in the subtree rooted at 'root'.

isIntDensityProfile() - Method in class sc.fiji.snt.analysis.sholl.Profile

isIntegerScale() - Method in class sc.fiji.snt.analysis.ColorMapper

Checks if the color mapping uses an integer scale.

isJustNearSlices() - Method in class sc.fiji.snt.TracerCanvas

isLabelImage(RandomAccessibleInterval<? extends RealType<?>>) - Static method in class sc.fiji.snt.util.ImgUtils

Checks whether a RandomAccessibleInterval appears to be a label image, using a default maximum of 500 classes.

isLabelImage(RandomAccessibleInterval<? extends RealType<?>>, int) - Static method in class sc.fiji.snt.util.ImgUtils

Checks whether a RandomAccessibleInterval appears to be a label (segmentation) image.

isLastUpdateFromLiveCheck() - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

Returns whether the most recent warning update originated from a live check (inline during tracing) as opposed to an on-demand or full scan.

isLeftHemisphere(double, double, double) - Static method in class sc.fiji.snt.annotation.AllenUtils

isLeftHemisphere(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils

Checks the hemisphere a neuron belongs to.

isLeftHemisphere(SNTPoint) - Static method in class sc.fiji.snt.annotation.AllenUtils

Checks the hemisphere a reconstruction node belongs to.

isLegacy3DViewerAvailable() - Static method in class sc.fiji.snt.gui.GuiUtils

isLegendVisible() - Method in class sc.fiji.snt.analysis.SNTChart

isListView() - Method in class sc.fiji.snt.gui.FileChooser

Checks if the current view type is list view.

isLiveSync() - Method in class sc.fiji.snt.viewer.BvvMultiSource

isMeshAvailable() - Method in class sc.fiji.snt.annotation.AllenCompartment

Checks whether a mesh is known to be available for this compartment.

isMeshAvailable() - Method in interface sc.fiji.snt.annotation.BrainAnnotation

Returns whether a mesh is available for this compartment.

isMeshAvailable() - Method in class sc.fiji.snt.annotation.DrosophilaCompartment

isMeshAvailable() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

isMeshBackfaceCull() - Method in class sc.fiji.snt.viewer.Viewer3D

Returns whether backface culling is enabled for OBJ meshes.

isModified() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

isMultiChannelRGB(ImgPlus<?>) - Static method in class sc.fiji.snt.util.ImgUtils

Checks if an ImgPlus appears to be a multi-channel RGB image (3 channels of 8-bit data, not packed ARGB).

isNaturalOrder() - Method in record class sc.fiji.snt.util.TreeUtils.EndpointMatch

Checks if the paths are in "natural" order for merging (p1.end → p2.start).

isNegative(Path) - Static method in class sc.fiji.snt.analysis.curation.CurationTags

isNeurolucidaXML(InputStream) - Static method in class sc.fiji.snt.io.NeurolucidaImporter

Checks whether the given input stream starts with Neurolucida XML content.

isNodeMapping() - Method in class sc.fiji.snt.analysis.TreeColorMapper

isNormDistributionVisible() - Method in class sc.fiji.snt.analysis.SNTChart

Gets whether a normal distribution curve is being overlaid over histogram frequencies

isOnlySelectedPathsVisible() - Method in class sc.fiji.snt.SNT

isOpen() - Static method in class sc.fiji.snt.plugin.GWDTMultiSomaCmd

Returns whether an instance of this dialog is currently visible.

isOpen() - Static method in class sc.fiji.snt.plugin.GWDTTracerCmd

Returns whether an instance of this dialog is currently visible.

isOutlineVisible() - Method in class sc.fiji.snt.analysis.SNTChart

Checks if the plot outline is visible.

isPanningEvent(MouseEvent) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphComponent

isParallelBranchPruneEnabled() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Returns whether parallel branch pruning is enabled.

isParentOf(BrainAnnotation) - Method in class sc.fiji.snt.annotation.AllenCompartment

Assesses if this annotation is the parent of the specified compartment.

isParentOf(BrainAnnotation) - Method in interface sc.fiji.snt.annotation.BrainAnnotation

Returns whether this compartment is a parent of parentCompartment.

isParentOf(BrainAnnotation) - Method in class sc.fiji.snt.annotation.DrosophilaCompartment

isParentOf(BrainAnnotation) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

isPathFittingEnabled() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Returns whether post-hoc path fitting is enabled.

isPaused() - Method in class sc.fiji.snt.gui.ScriptRecorder

Returns whether recording is currently paused.

isPointVisible(ImagePlus, int, int) - Static method in class sc.fiji.snt.util.ImpUtils

Checks if a given point (in image coordinates) is currently visible in an image

isPositive(Path) - Static method in class sc.fiji.snt.analysis.curation.CurationTags

isPrimary() - Method in class sc.fiji.snt.Path

Checks if this Path is root.

isPrimaryBranchesInferred() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Checks whether the number of primary branches is being inferred from the number of intersections at starting radius or if it has been set explicitly.

isQuartilesVisible() - Method in class sc.fiji.snt.analysis.SNTChart

Gets whether quartile markers (Q1, Median, Q3) are being overlaid over histogram frequencies

isReady() - Method in class sc.fiji.snt.SNTUI

Assesses whether the UI is blocked.

isReal() - Method in class sc.fiji.snt.util.PointInImage

isReconstructionFile(File) - Static method in class sc.fiji.snt.SNTUtils

isReplacePaths() - Method in class sc.fiji.snt.gui.SWCImportDialog

isRetrieveIntDensitiesSet() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

isReviewed(Path) - Static method in class sc.fiji.snt.analysis.curation.CurationTags

isRGB(ImgPlus<?>) - Static method in class sc.fiji.snt.util.ImgUtils

Checks if an ImgPlus contains packed RGB data (ARGBType).

isSameLocation(PointInImage) - Method in class sc.fiji.snt.util.PointInImage

isSaveCompressedTraces() - Method in class sc.fiji.snt.SNTPrefs

Checks if traces should be saved in compressed format.

isSaveWinLocations() - Method in class sc.fiji.snt.SNTPrefs

Checks if window locations should be saved and restored.

isScaled() - Method in class sc.fiji.snt.util.BoundingBox

Checks whether this BoundingBox is spatially calibrated, i.e., if voxel spacing has been specified

isSciViewAvailable() - Static method in class sc.fiji.snt.gui.cmds.EnableSciViewUpdateSiteCmd

isSecondaryDataAvailable() - Method in class sc.fiji.snt.SNT

Assesses if the 'secondary image' has been loaded into memory.

isSecondaryImageFileLoaded() - Method in class sc.fiji.snt.SNT

isSegmented(ImagePlus) - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

Checks whether the given image is binary (segmented) or thresholded.

isSelected() - Method in class sc.fiji.snt.gui.CheckboxSpinner

isSelected() - Method in class sc.fiji.snt.Path

isSelected(String) - Method in class sc.fiji.snt.gui.cmds.AutoTraceConfigDialog

Whether the row with the given parameter key is checked for application.

isSelected(Path) - Method in class sc.fiji.snt.PathAndFillManager

Checks if a Path is currently selected in the GUI.

isSelected(SeedPoint) - Method in class sc.fiji.snt.seed.SeedOverlay

isShowDirectionArrows() - Static method in class sc.fiji.snt.PathNodeCanvas

Gets whether direction arrows are currently being displayed.

isShowing() - Method in class sc.fiji.snt.BookmarkManager

isSkipSingleVoxels() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser3D

isSkipSomaticSegments() - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

isSNTInstance() - Method in class sc.fiji.snt.viewer.Viewer3D

Checks whether this instance is SNT's Reconstruction Viewer.

isSomaDisplayTriangle() - Method in class sc.fiji.snt.SNTPrefs

Sets whether single-node paths tagged as are rendered w/ triangular shape.

isSplitDendritesFromAxons() - Method in class sc.fiji.snt.viewer.Viewer3D

Checks whether axons and dendrites of imported Trees are set to be imported as separated objects.

isStandaloneContext() - Static method in class sc.fiji.snt.SNTUtils

Returns whether the current context was self-initialized by SNT (i.e., no host application like ImageJ/Fiji provided one).

isSummarized() - Method in class sc.fiji.snt.analysis.SNTTable

Checks if the table contains summary statistics.

isTracingOnSecondaryImageActive() - Method in class sc.fiji.snt.SNT

isTracingOnSecondaryImageAvailable() - Method in class sc.fiji.snt.SNT

isTypeDefined() - Method in class sc.fiji.snt.util.SNTColor

Checks if an SWC type has been defined.

isUIready() - Method in class sc.fiji.snt.SNT

isUnsavedChanges() - Method in class sc.fiji.snt.SNT

isUnsure(Path) - Static method in class sc.fiji.snt.analysis.curation.CurationTags

isUseAbsoluteWindowSize() - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Gets whether absolute window size is used instead of fractional window size.

isUseGlobalThresholds() - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Gets whether global thresholds are used for phase classification.

isUsePathRadius() - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Gets whether to use path radius for thickness calculation.

isUseSubVolumeStats - Variable in class sc.fiji.snt.SNT

isUsingCumulativeFrequencies() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

isValid() - Method in class sc.fiji.snt.analysis.TreeStatistics

Checks whether this tree is topologically valid, i.e., contains only one root and no loops.

isValidURL(String) - Static method in class sc.fiji.snt.SNTUtils

isVerbose() - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Checks if verbose logging is enabled.

isVertexLabelsEnabled() - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter

isVirtualStack(ImagePlus) - Static method in class sc.fiji.snt.util.ImpUtils

isVisible() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

isVisible() - Static method in class sc.fiji.snt.gui.cmds.ShortcutWindowCmd

isVisible() - Method in class sc.fiji.snt.seed.SeedOverlay

isVisible() - Method in class sc.fiji.snt.viewer.Bvv.AnnotationOverlay

isZoomAllPanesDisabled() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

ITALIC - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

itemWithoutAccelerator(String) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

iterateNeighbors(int[], int, int, Runnable) - Static method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Iterates over all neighbor offsets (26-connectivity in 3D).

iterateNeighborsForFM(long[], long[], int, double[], DoubleConsumer) - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

Iterate over neighbors with connectivity filtering.

iterator() - Method in class sc.fiji.snt.tracing.image.ArraySearchImage

iterator() - Method in class sc.fiji.snt.tracing.image.ListSearchImage

iterator() - Method in class sc.fiji.snt.tracing.image.MapSearchImage

iterator() - Method in class sc.fiji.snt.tracing.image.SearchImageStack

J

JOINT - Static variable in class sc.fiji.snt.PathNodeCanvas

Flag describing a fork point node

jointLeafPruneEnabled - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

JSONImporterCmd - Class in sc.fiji.snt.gui.cmds

Command for importing a (MouseLight) JSON file

JSONImporterCmd() - Constructor for class sc.fiji.snt.gui.cmds.JSONImporterCmd

jumpFwd(long) - Method in class sc.fiji.snt.util.CircleCursor3D

jumpFwd(long) - Method in class sc.fiji.snt.util.PathCursor

just_near_slices - Variable in class sc.fiji.snt.TracerCanvas

justDisplayNearSlices(boolean, int) - Method in class sc.fiji.snt.SNT

K

kappa() - Method in record class sc.fiji.snt.analysis.CircularModels.VonMisesFit

Returns the value of the kappa record component.

kappaFromRBar(double) - Static method in class sc.fiji.snt.analysis.CircularModels

Returns κ from \bar R using standard fast approximations as per Fisher et. al., Statistical Analysis of Spherical Data and Matlab's CircStat package by Philipp Berens

KEY_2D3D - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

KEY_CALIBRATION - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

KEY_CENTER - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

KEY_CHANNEL_POS - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

KEY_COLOR - Static variable in interface sc.fiji.snt.TreeProperties

KEY_COMPARTMENT - Static variable in interface sc.fiji.snt.TreeProperties

KEY_EFFECTIVE_STEP_SIZE - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

KEY_EXTRA_MEASUREMENT - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

KEY_FRAME_POS - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

KEY_FRAME_POS - Static variable in interface sc.fiji.snt.TreeProperties

KEY_HEMISHELLS - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

KEY_ID - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

KEY_ID - Static variable in interface sc.fiji.snt.TreeProperties

KEY_IMG - Static variable in interface sc.fiji.snt.TreeProperties

KEY_IMG_CHANNEL - Static variable in interface sc.fiji.snt.TreeProperties

KEY_IMG_FRAME - Static variable in interface sc.fiji.snt.TreeProperties

KEY_LABEL - Static variable in interface sc.fiji.snt.TreeProperties

KEY_NSAMPLES - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

KEY_NSAMPLES_INTG - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

KEY_SLICE_POS - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

KEY_SOURCE - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

KEY_SOURCE - Static variable in interface sc.fiji.snt.TreeProperties

KEY_SPATIAL_UNIT - Static variable in interface sc.fiji.snt.TreeProperties

KEY_THRESHOLD_RANGE - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

KEYBOARD - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

keyboardCheatSheetButton() - Static method in class sc.fiji.snt.gui.GuiUtils.Buttons

keyboardHandler - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor

Key Classes - Search tag in package sc.fiji.snt.tracing.auto

Section

Keyframe(String) - Constructor for class sc.fiji.snt.viewer.Bvv.Keyframe

Convenience constructor that deserializes a keyframe from a string.

Keyframe(AffineTransform3D, double, double, double, Set<String>, int) - Constructor for class sc.fiji.snt.viewer.Bvv.Keyframe

Keyframe(AffineTransform3D, double, double, double, Set<String>, int, int) - Constructor for class sc.fiji.snt.viewer.Bvv.Keyframe

keySet() - Method in class sc.fiji.snt.tracing.image.SearchImageStack

KIWI_BIRD - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

L

label() - Method in class sc.fiji.snt.viewer.OBJMesh

Gets this mesh label.

LABEL - Enum constant in enum class sc.fiji.snt.FillConverter.ResultType

LabelProximityDetector - Class in sc.fiji.snt.analysis.detection

Detects contact points between traced paths and labeled surfaces (from a segmentation/label image).

LabelProximityDetector.Config - Class in sc.fiji.snt.analysis.detection

Configuration for LabelProximityDetector.

LabelProximityDetectorCmd - Class in sc.fiji.snt.gui.cmds

SciJava command for detecting proximity contacts between traced paths and labeled surfaces (segmentation images).

LabelProximityDetectorCmd() - Constructor for class sc.fiji.snt.gui.cmds.LabelProximityDetectorCmd

LabelsToSeeds - Class in sc.fiji.snt.seed

Helper that turns a labels image (e.g. cellpose, Labkit, StarDist segmentation output) into a list of SeedPoints, one per non-zero label.

labelValue - Variable in class sc.fiji.snt.analysis.detection.Detection

Label value from a segmentation/label image associated with this detection, or -1 if not applicable.

LabkitLoaderCmd - Class in sc.fiji.snt.plugin

Command for sending Path-converted ROIs to a new Labkit instance.

LabkitLoaderCmd() - Constructor for class sc.fiji.snt.plugin.LabkitLoaderCmd

LAF_DARCULA - Static variable in class sc.fiji.snt.gui.GuiUtils

LAF_DARK - Static variable in class sc.fiji.snt.gui.GuiUtils

LAF_DEFAULT - Static variable in class sc.fiji.snt.gui.GuiUtils

LAF_LIGHT - Static variable in class sc.fiji.snt.gui.GuiUtils

LAF_LIGHT_INTJ - Static variable in class sc.fiji.snt.gui.GuiUtils

LAG - Enum constant in enum class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhaseType

Lag phase - slow positive growth

last_start_point_x - Variable in class sc.fiji.snt.SNT

last_start_point_y - Variable in class sc.fiji.snt.SNT

last_start_point_z - Variable in class sc.fiji.snt.SNT

lastDstats - Variable in class sc.fiji.snt.analysis.TreeStatistics

lastDstatsCanBeRecycled(String) - Method in class sc.fiji.snt.analysis.TreeStatistics

lastKnownDir() - Static method in class sc.fiji.snt.SNTPrefs

lastNode() - Method in class sc.fiji.snt.Path

Returns the last node of this path.

lastPathResult - Variable in class sc.fiji.snt.tracing.TubularGeodesicsTracer

lastReportMilliseconds - Variable in class sc.fiji.snt.tracing.SearchThread

launchSigmaPaletteAround(int, int) - Method in class sc.fiji.snt.SNTUI

LAYERS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

LAYOUT_BIOFORMATS2RAW - Static variable in class sc.fiji.snt.io.OmeAxisUtils

Layout type for bioformats2raw converted files

LAYOUT_OME_NGFF - Static variable in class sc.fiji.snt.io.OmeAxisUtils

Layout type for native OME-NGFF files

LAYOUT_UNKNOWN - Static variable in class sc.fiji.snt.io.OmeAxisUtils

Unknown layout type

Lazy - Class in sc.fiji.snt.filter

Static helpers for creating lazy filtered images

LEAF_ONLY_FORMATTER - Static variable in class sc.fiji.snt.gui.OntologyBrowser

A predefined path formatter that returns only the leaf node's name.

leafPruneEnabled - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

leafPruneOverlap - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

LEFT_HEMISPHERE - Static variable in interface sc.fiji.snt.annotation.BrainAnnotation

Character constant representing the left hemisphere

leftAlignedLabel(String, boolean) - Static method in class sc.fiji.snt.gui.GuiUtils

leftAlignedLabel(String, String, boolean) - Static method in class sc.fiji.snt.gui.GuiUtils

length - Variable in class sc.fiji.snt.analysis.sholl.ProfileEntry

The total cable length associated with this entry's radius

length() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.TimePoint

Returns the value of the length record component.

LENGTH - Enum constant in enum class sc.fiji.snt.analysis.sholl.math.ShollStats.DataMode

LENGTH - Static variable in class sc.fiji.snt.analysis.graph.AnnotationGraph

LENGTH - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Cable length"

lengthChange() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.ElongationEvent

Returns the value of the lengthChange record component.

lengthChange() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhase

Returns the value of the lengthChange record component.

lengthChange() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.RetractionEvent

Returns the value of the lengthChange record component.

lengths() - Method in class sc.fiji.snt.analysis.sholl.Profile

lengthsAsArray() - Method in class sc.fiji.snt.analysis.sholl.Profile

lengthThreshold - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

lengthThreshold - Variable in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

libraryPane - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor

lightDarkToggleButton() - Method in class sc.fiji.snt.gui.SNTEditorPane

LinAlgUtils - Class in sc.fiji.snt.util

Static methods for linear algebra

LINE - Enum constant in enum class sc.fiji.snt.analysis.ProfileProcessor.Shape

LINE2D - Static variable in class sc.fiji.snt.analysis.PathProfiler

LINE3D - Static variable in class sc.fiji.snt.analysis.PathProfiler

LinearProfileStats - Class in sc.fiji.snt.analysis.sholl.math

Retrieves descriptive statistics and calculates Sholl Metrics from sampled Sholl profiles, including those relying on polynomial fitting.

LinearProfileStats(Profile) - Constructor for class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Instantiates the Linear Profile Statistics.

LinearProfileStats(Profile, ShollStats.DataMode) - Constructor for class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Instantiates the Linear Profile Statistics.

LINES_LEANING - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

LINK - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

linkColor() - Static method in class sc.fiji.snt.gui.GuiUtils

list() - Method in class sc.fiji.snt.seed.SeedOverlay

Returns a defensive snapshot of all held seeds (a fresh ArrayList, safe to iterate while the overlay continues to mutate on another thread).

list() - Method in class sc.fiji.snt.Tree

Gets all the paths from this tree.

LIST - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

LIST_ALT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

listCurationFiles(File) - Static method in class sc.fiji.snt.analysis.curation.PlausibilityCalibrator

Lists all .curation files in the curations subdirectory of the given workspace directory.

listeners - Variable in class sc.fiji.snt.SNT

listFromDir(String) - Static method in class sc.fiji.snt.Tree

Retrieves a list of Trees from reconstruction files stored in a common directory.

listFromDir(String, String) - Static method in class sc.fiji.snt.Tree

Retrieves a list of Trees from reconstruction files stored in a common directory matching the specified criteria.

listFromDir(String, String, String...) - Static method in class sc.fiji.snt.Tree

Retrieves a list of Trees from reconstruction files stored in a common directory matching the specified criteria.

listFromFile(String) - Static method in class sc.fiji.snt.Tree

Retrieves a list of Trees from a single file.

listIcon(JList<?>, IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory

listProfileEntries() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollTable

Lists (details) the Profile entries.

ListSearchImage<V> - Class in sc.fiji.snt.tracing.image

A SearchImage backed by an ImgLib2 ListImg, providing list-based storage for path-search data structures.

ListSearchImage(Class<V>, int, int) - Constructor for class sc.fiji.snt.tracing.image.ListSearchImage

ListSearchImageSupplier(Class<V>, int, int) - Constructor for class sc.fiji.snt.tracing.image.SupplierUtil.ListSearchImageSupplier

LiveCheck() - Constructor for class sc.fiji.snt.analysis.curation.PlausibilityCheck.LiveCheck

load() - Method in class sc.fiji.snt.gui.DemoRunner.Demo

load(int) - Method in class sc.fiji.snt.gui.DemoRunner

load(Roi[]) - Method in class sc.fiji.snt.BookmarkManager

load(File) - Method in class sc.fiji.snt.BookmarkManager

Loads bookmarks from the specified file.

load(File) - Method in class sc.fiji.snt.NotesUI

load(File, PlausibilityMonitor) - Static method in class sc.fiji.snt.analysis.curation.PlausibilityCalibrator

Loads thresholds and enabled states from a .curation properties file and applies them to the given monitor.

load(String) - Method in class sc.fiji.snt.BookmarkManager

load(String, int...) - Method in class sc.fiji.snt.PathAndFillManager

Imports a reconstruction file (any supported extension).

load(List<Roi>) - Method in class sc.fiji.snt.BookmarkManager

Loads bookmarks from the specified list of ROIs.

load(List<Roi>) - Method in class sc.fiji.snt.DelineationsManager

Loads delineations from a list of area ROIs.

load(SingleCellArrayImg<S, ?>) - Method in class sc.fiji.snt.filter.UnaryComputerOpCellLoader

loadBuiltIn(String, PlausibilityMonitor) - Static method in class sc.fiji.snt.analysis.curation.PlausibilityCalibrator

Loads a built-in curation preset bundled in the SNT JAR and applies it to the given monitor.

loadCompressedXML(String) - Method in class sc.fiji.snt.PathAndFillManager

LOADED - Enum constant in enum class sc.fiji.snt.FillManagerUI.State

loader - Variable in class sc.fiji.snt.viewer.OBJMesh

loadGraph(DirectedWeightedGraph) - Method in class sc.fiji.snt.SNTService

loadGuessingType(String) - Method in class sc.fiji.snt.PathAndFillManager

loadGuessingType(String, InputStream) - Method in class sc.fiji.snt.PathAndFillManager

loadHints() - Method in class sc.fiji.snt.gui.GuiUtils

loadImagefromGUI(int, int) - Method in class sc.fiji.snt.SNTUI

LOADING - Static variable in class sc.fiji.snt.SNTUI

Flag specifying UI is currently waiting for I/0 operations to conclude

loadLabelsFile(String) - Method in class sc.fiji.snt.SNT

loadMesh(String, ColorRGB, double) - Method in class sc.fiji.snt.viewer.Viewer3D

Loads a Wavefront .OBJ file.

LoadObjCmd - Class in sc.fiji.snt.gui.cmds

Command for loading an OBJ file in Reconstruction Viewer

LoadObjCmd() - Constructor for class sc.fiji.snt.gui.cmds.LoadObjCmd

loadPluginPrefs() - Method in class sc.fiji.snt.SNTPrefs

LoadReconstructionCmd - Class in sc.fiji.snt.gui.cmds

Command for loading Reconstruction files in Reconstruction Viewer.

LoadReconstructionCmd() - Constructor for class sc.fiji.snt.gui.cmds.LoadReconstructionCmd

loadRefBrain(String) - Method in class sc.fiji.snt.viewer.Viewer3D

Loads the surface mesh of a supported reference brain/neuropil.

loadRoisFromZip(File) - Static method in class sc.fiji.snt.analysis.RoiConverter

loadSecondaryImage(ImagePlus) - Method in class sc.fiji.snt.SNT

loadSecondaryImage(ImagePlus, boolean) - Method in class sc.fiji.snt.SNT

loadSecondaryImage(File) - Method in class sc.fiji.snt.SNT

Loads the 'secondary image' specified by SNT.setSecondaryImage(File) into memory as 32-bit data.

loadSecondaryImage(RandomAccessibleInterval<T>, boolean) - Method in class sc.fiji.snt.SNT

loadSecondaryImage(RandomAccessibleInterval<T>, boolean, boolean) - Method in class sc.fiji.snt.SNT

LoadSeedsFromLabelsImageCmd - Class in sc.fiji.snt.gui.cmds

Generates SeedPoints from an open labels image (e.g. cellpose, Labkit, StarDist masks).

LoadSeedsFromLabelsImageCmd() - Constructor for class sc.fiji.snt.gui.cmds.LoadSeedsFromLabelsImageCmd

LoadSeedsFromROIsCmd - Class in sc.fiji.snt.gui.cmds

Generates SeedPoints from the contents of the RoiManager.

LoadSeedsFromROIsCmd() - Constructor for class sc.fiji.snt.gui.cmds.LoadSeedsFromROIsCmd

loadStartupPrefs() - Method in class sc.fiji.snt.SNTPrefs

Deprecated.

loadSWCFile(File) - Method in class sc.fiji.snt.SNT

loadTracesFile(File) - Method in class sc.fiji.snt.SNT

Assumes UI is available

loadTracings(File) - Method in class sc.fiji.snt.SNT

loadTracings(String) - Method in class sc.fiji.snt.SNTService

Loads the specified tracings file.

loadTree(Tree) - Method in class sc.fiji.snt.SNTService

Loads the specified tree.

loadTrees(Collection<Tree>) - Method in class sc.fiji.snt.SNTService

Loads the specified collection of trees.

loadUncompressedXML(String) - Method in class sc.fiji.snt.PathAndFillManager

localize(double[]) - Method in class sc.fiji.snt.util.CircleCursor3D

localize(double[]) - Method in class sc.fiji.snt.util.PathCursor

localize(float[]) - Method in class sc.fiji.snt.util.CircleCursor3D

localize(float[]) - Method in class sc.fiji.snt.util.PathCursor

localize(int[]) - Method in class sc.fiji.snt.util.CircleCursor3D

localize(int[]) - Method in class sc.fiji.snt.util.PathCursor

localize(long[]) - Method in class sc.fiji.snt.util.CircleCursor3D

localize(long[]) - Method in class sc.fiji.snt.util.PathCursor

LocalThicknessCmd - Class in sc.fiji.snt.plugin

Convenience command for running Fiji's "Local Thickness" plugin from SNT, enabling estimation of radii from binary skeleton images.

LocalThicknessCmd() - Constructor for class sc.fiji.snt.plugin.LocalThicknessCmd

location() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCheck.Warning

Returns the value of the location record component.

LOCK - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

LOCK_OPEN - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

log(String) - Static method in class sc.fiji.snt.SNTUtils

log(String) - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Logs a message if verbose mode is enabled.

LOG_LOG - Static variable in interface sc.fiji.snt.analysis.sholl.math.ShollStats

Flag for imposing Log-log analysis

logger - Variable in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

logger - Variable in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

logger - Variable in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Logger - Class in sc.fiji.snt.util

The Logger class provides functionality for logging messages with different levels such as info, debug, and warn.

Logger(Class<?>) - Constructor for class sc.fiji.snt.util.Logger

Logger(Context, String) - Constructor for class sc.fiji.snt.util.Logger

Constructs a new Logger with the specified context and caller identifier.

logSceneControls() - Method in class sc.fiji.snt.viewer.Viewer3D

Logs API calls controlling the scene (view point, bounds, etc.) to Script Recorder (or Console if Script Recorder is not running).

longPos - Variable in class sc.fiji.snt.util.CircleCursor3D

longSmallMsg(String, Component) - Static method in class sc.fiji.snt.gui.GuiUtils

loops - Variable in class sc.fiji.snt.tracing.SearchThread

loops_at_last_report - Variable in class sc.fiji.snt.tracing.SearchThread

loopSolvingChoice - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

lowerT - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

LOWEST_INTENSITY_BRANCH - Static variable in class sc.fiji.snt.tracing.auto.BinaryTracer

Pruning mode: flag for lowest intensity branch pruning

LOWEST_INTENSITY_VOXEL - Static variable in class sc.fiji.snt.tracing.auto.BinaryTracer

Pruning mode: flag for lowest pixel intensity pruning.

LSystemsTree - Class in sc.fiji.snt.util

Lindenmayer systems utilities for rendering fractal trees using L-system rules for generating and visualizing self-similar branching structures.

LSystemsTree() - Constructor for class sc.fiji.snt.util.LSystemsTree

lutChoiceChanged() - Method in class sc.fiji.snt.plugin.ShollAnalysisTreeCmd

luts - Variable in class sc.fiji.snt.analysis.ColorMapper

lutService - Variable in class sc.fiji.snt.analysis.ColorMapper

M

MAGIC - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

MAGNIFIED_LOCATION - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

main(String[]) - Static method in class sc.fiji.snt.analysis.ConvexHull2D

main(String[]) - Static method in class sc.fiji.snt.analysis.ConvexHull3D

main(String[]) - Static method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

Main method for testing and demonstration purposes.

main(String[]) - Static method in class sc.fiji.snt.analysis.graph.AnnotationGraph

main(String[]) - Static method in class sc.fiji.snt.analysis.graph.GraphUtils

main(String[]) - Static method in class sc.fiji.snt.analysis.GroupedTreeStatistics

main(String...) - Static method in class sc.fiji.snt.analysis.MultiTreeColorMapper

main(String[]) - Static method in class sc.fiji.snt.analysis.MultiTreeStatistics

Main method for testing and demonstration purposes.

main(String...) - Static method in class sc.fiji.snt.analysis.NodeColorMapper

main(String[]) - Static method in class sc.fiji.snt.analysis.NodeProfiler

main(String[]) - Static method in class sc.fiji.snt.analysis.NodeStatistics

main(String[]) - Static method in class sc.fiji.snt.analysis.PathProfiler

main(String[]) - Static method in class sc.fiji.snt.analysis.PathStraightener

Main method for testing and demonstration purposes.

main(String[]) - Static method in class sc.fiji.snt.analysis.PersistenceAnalyzer

main(String[]) - Static method in class sc.fiji.snt.analysis.ProfileProcessor

main(String[]) - Static method in class sc.fiji.snt.analysis.RootAngleAnalyzer

main(String...) - Static method in class sc.fiji.snt.analysis.sholl.parsers.TabularParser

main(String...) - Static method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

main(String[]) - Static method in class sc.fiji.snt.analysis.ShollAnalyzer

main(String[]) - Static method in class sc.fiji.snt.analysis.SNTChart

main(String[]) - Static method in class sc.fiji.snt.analysis.StrahlerAnalyzer

main(String...) - Static method in class sc.fiji.snt.analysis.TreeColorMapper

main(String[]) - Static method in class sc.fiji.snt.analysis.TreeStatistics

main(String[]) - Static method in class sc.fiji.snt.annotation.AllenCompartment

main(String[]) - Static method in class sc.fiji.snt.annotation.AllenUtils

main(String[]) - Static method in class sc.fiji.snt.annotation.VFBUtils

main(String[]) - Static method in class sc.fiji.snt.FillManagerUI

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.AddTextAnnotationCmd

IDE debug method.

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.AnnotationGraphGeneratorCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.AnnotationGraphRecViewerCmd

main(String...) - Static method in class sc.fiji.snt.gui.cmds.ChooseDatasetCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.ColorMapReconstructionCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.CompareFilesCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.ComputeSecondaryImg

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.CustomizeLegendCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.CustomizeObjCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.CustomizeTreeCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.DistributionBPCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.DistributionCPCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.DuplicateCmd

main(String...) - Static method in class sc.fiji.snt.gui.cmds.EnableSciViewUpdateSiteCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.FilterOrTagPathsByAngleCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.GraphGeneratorCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.InsectBrainImporterCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.JSONImporterCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.LoadObjCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.LoadReconstructionCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.MLImporterCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.MultiSWCImporterCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.mxOrganicLayoutPrefsCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.NDFImporterCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.NewGraphOptionsCmd

main(String...) - Static method in class sc.fiji.snt.gui.cmds.OpenDatasetCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.PathFitterCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.PrefsCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.ReconstructionViewerCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.RecViewerPrefsCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.RemoteSWCImporterCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.ShowCorrespondencesCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.SNTLoaderCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.SWCTypeFilterCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.SWCTypeOptionsCmd

main(String[]) - Static method in class sc.fiji.snt.gui.cmds.TranslateReconstructionsCmd

main(String[]) - Static method in class sc.fiji.snt.gui.ColorChooserButton

main(String[]) - Static method in class sc.fiji.snt.gui.ColorMenu

main(String[]) - Static method in class sc.fiji.snt.gui.MeasureUI

main(String[]) - Static method in class sc.fiji.snt.gui.PathManagerUISearchableBar

main(String[]) - Static method in class sc.fiji.snt.gui.ScriptRecorder

main(String[]) - Static method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

main(String...) - Static method in class sc.fiji.snt.io.FlyCircuitLoader

main(String...) - Static method in class sc.fiji.snt.io.InsectBrainLoader

main(String...) - Static method in class sc.fiji.snt.io.MouseLightLoader

main(String...) - Static method in class sc.fiji.snt.io.MouseLightQuerier

main(String...) - Static method in class sc.fiji.snt.io.NDFImporter

main(String...) - Static method in class sc.fiji.snt.io.NeuroMorphoLoader

main(String[]) - Static method in class sc.fiji.snt.PathManagerUI

main(String[]) - Static method in class sc.fiji.snt.plugin.AnalyzerCmd

Deprecated.

main(String[]) - Static method in class sc.fiji.snt.plugin.AnnotationDensityCmd

main(String[]) - Static method in class sc.fiji.snt.plugin.BrainAnnotationCmd

main(String[]) - Static method in class sc.fiji.snt.plugin.ConvexHullCmd

main(String[]) - Static method in class sc.fiji.snt.plugin.GroupAnalyzerCmd

main(String[]) - Static method in class sc.fiji.snt.plugin.ij1.Strahler

IDE Debug method

main(String[]) - Static method in class sc.fiji.snt.plugin.InterpolateRadiiCmd

main(String[]) - Static method in class sc.fiji.snt.plugin.LocalThicknessCmd

main(String[]) - Static method in class sc.fiji.snt.plugin.PathAnalyzerCmd

main(String[]) - Static method in class sc.fiji.snt.plugin.PathMatcherCmd

main(String[]) - Static method in class sc.fiji.snt.plugin.PathSpineAnalysisCmd

main(String[]) - Static method in class sc.fiji.snt.plugin.PathTimeAnalysisCmd

main(String[]) - Static method in class sc.fiji.snt.plugin.PlotterCmd

main(String[]) - Static method in class sc.fiji.snt.plugin.ROIExporterCmd

main(String...) - Static method in class sc.fiji.snt.plugin.ShollAnalysisBulkTreeCmd

main(String...) - Static method in class sc.fiji.snt.plugin.ShollAnalysisTreeCmd

main(String[]) - Static method in class sc.fiji.snt.plugin.SkeletonizerCmd

main(String[]) - Static method in class sc.fiji.snt.plugin.StrahlerCmd

main(String[]) - Static method in class sc.fiji.snt.plugin.TreeMapperCmd

main(String[]) - Static method in class sc.fiji.snt.SciViewSNT

main(String[]) - Static method in class sc.fiji.snt.tracing.auto.BinaryTracer

main(String[]) - Static method in class sc.fiji.snt.tracing.auto.GWDTTracer

main(String[]) - Static method in class sc.fiji.snt.Tree

main(String[]) - Static method in class sc.fiji.snt.viewer.GraphViewer

main(String...) - Static method in class sc.fiji.snt.viewer.MultiViewer2D

main(String...) - Static method in class sc.fiji.snt.viewer.MultiViewer3D

main(String...) - Static method in class sc.fiji.snt.viewer.Viewer2D

makeBorderless(AbstractButton...) - Static method in class sc.fiji.snt.gui.GuiUtils.Buttons

makePalette(int, int, int, int, int, int, double[], int, int, int) - Method in class sc.fiji.snt.gui.SigmaPalette

Displays the Sigma wizard in a separate thread.

makePathVolume(Collection<Path>, boolean) - Method in class sc.fiji.snt.SNT

Rasterizes centerline of paths into an ImagePlus

manualRadius - Variable in class sc.fiji.snt.SNT

ManualTracerThread - Class in sc.fiji.snt.tracing

A tracer thread for manual tracing.

ManualTracerThread(SNT, double, double, double, double, double, double) - Constructor for class sc.fiji.snt.tracing.ManualTracerThread

map(String, String) - Method in class sc.fiji.snt.analysis.NodeColorMapper

Maps nodes after the specified measurement.

map(String, ColorTable) - Method in class sc.fiji.snt.analysis.AnnotationMapper

Maps annotation properties to colors using the specified color table.

map(String, ColorTable) - Method in class sc.fiji.snt.analysis.ColorMapper

Sets up the color mapping for the specified measurement using the given color table.

map(String, ColorTable) - Method in class sc.fiji.snt.analysis.MultiTreeColorMapper

map(String, ColorTable) - Method in class sc.fiji.snt.analysis.NodeColorMapper

Maps nodes after the specified measurement.

map(Collection<? extends PointInImage>, String, String) - Method in class sc.fiji.snt.analysis.TreeColorMapper

Colorizes a collection of points after the specified measurement.

map(SNTGraph<V, E>, String, String) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

map(SNTGraph<V, E>, String, ColorTable) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

map(SNTGraph<V, E>, AsSubgraph<V, E>, String, ColorTable) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

map(Tree, String, String) - Method in class sc.fiji.snt.analysis.TreeColorMapper

Colorizes a tree after the specified measurement.

map(Tree, String, ColorTable) - Method in class sc.fiji.snt.analysis.TreeColorMapper

Colorizes a tree after the specified measurement.

map(Tree, LinearProfileStats, ColorTable) - Method in class sc.fiji.snt.analysis.TreeColorMapper

Colorizes a tree using Sholl data.

map(Tree, Profile, ColorTable) - Method in class sc.fiji.snt.analysis.TreeColorMapper

Colorizes a tree using Sholl data.

MAP - Enum constant in enum class sc.fiji.snt.SNT.SearchImageType

MAP_PIN - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

mapRootDistanceToCentroid(AllenCompartment, ColorTable) - Method in class sc.fiji.snt.analysis.MultiTreeColorMapper

MapSearchImage<V> - Class in sc.fiji.snt.tracing.image

A sparse matrix implementation backed by a Long2ObjectOpenHashMap

MapSearchImage() - Constructor for class sc.fiji.snt.tracing.image.MapSearchImage

MapSearchImageSupplier() - Constructor for class sc.fiji.snt.tracing.image.SupplierUtil.MapSearchImageSupplier

mapToBetweennessCentrality(ColorTable) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

mapToConnectivity(ColorTable) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

mapToEccentricity(ColorTable) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

mapToEdgeWeight(ColorTable) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

mapToHeavyPathDecomposition(ColorTable) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

mapToIncomingWeight(ColorTable) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

mapToInDegree(ColorTable) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

mapToOutDegree(ColorTable) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

mapToOutgoingWeight(ColorTable) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

mapToPageRank(ColorTable) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

mapToProperty(String, ColorTable) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

mapToProperty(String, ColorTable) - Method in class sc.fiji.snt.analysis.TreeColorMapper

mapTrees(List<Tree>, String) - Method in class sc.fiji.snt.analysis.TreeColorMapper

Colorizes a list of trees, with each tree being assigned a LUT index.

MARKER - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

markNegative(Path) - Static method in class sc.fiji.snt.analysis.curation.CurationTags

Tags path as a negative (rejected) review example.

markPoint(ShollPoint, int, int) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

Highlights a point on a plot without listing it on the Plot's table.

markPoint(ShollPoint, Color) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

Highlights a point on a plot using the default marker.

markPositive(Path) - Static method in class sc.fiji.snt.analysis.curation.CurationTags

Tags path as a positive (accepted) review example.

markUnsure(Path) - Static method in class sc.fiji.snt.analysis.curation.CurationTags

Tags path as needing follow-up review ("not sure").

mask() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Returns the value of the mask record component.

maskImgFileBeingProcessed - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

MASKS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

matches(NeuriteGrowthData) - Method in interface sc.fiji.snt.analysis.growth.GrowthAnalysisResults.NeuriteSelectionCriterion

MATH - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

max - Variable in class sc.fiji.snt.analysis.ColorMapper

max() - Method in class sc.fiji.snt.analysis.RootAngleAnalyzer

MAX - Enum constant in enum class sc.fiji.snt.analysis.ProfileProcessor.Metric

MAX - Static variable in class sc.fiji.snt.analysis.ShollAnalyzer

MAX_FITTED - Static variable in class sc.fiji.snt.analysis.ShollAnalyzer

MAX_FITTED_RADIUS - Static variable in class sc.fiji.snt.analysis.ShollAnalyzer

MAX_INTENSITY_KEY - Static variable in class sc.fiji.snt.gui.cmds.MultiSpectralRefinerCmd

MAX_N_SPANS - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D

MAX_PERCENT - Static variable in class sc.fiji.snt.gui.GuiUtils.JTables.VisitingZoom

MAX_PERCENT_C_KEY - Static variable in class sc.fiji.snt.gui.cmds.MultiSpectralRefinerCmd

MAX_RADIUS_KEY - Static variable in class sc.fiji.snt.gui.cmds.MultiSpectralRefinerCmd

MAX_SEARCH_RADIUS_PX_KEY - Static variable in class sc.fiji.snt.gui.cmds.PathFitterCmd

MAX_SNAP_CURSOR_WINDOW_XY - Static variable in class sc.fiji.snt.SNT

MAX_SNAP_CURSOR_WINDOW_Z - Static variable in class sc.fiji.snt.SNT

MAX_UNDO_STEPS - Static variable in class sc.fiji.snt.SNTPrefs

maxBounds - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

maxConnectDist - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

maxDimension(long[]) - Static method in class sc.fiji.snt.util.ImgUtils

maximumDistanceCompletelyExplored(FillerThread, double) - Method in interface sc.fiji.snt.FillerProgressCallback

maximumDistanceCompletelyExplored(FillerThread, double) - Method in class sc.fiji.snt.FillManagerUI

maxIntensity - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

maxIntensityProjection(RandomAccessibleInterval<RealType<?>>) - Static method in class sc.fiji.snt.util.ImgUtils

Computes a max-intensity projection along the third dimension (Z) of a 3D image, returning a 2D Img with the same XY extent.

maxIntensityThreshold() - Method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Returns the value of the maxIntensityThreshold record component.

maxIterations - Variable in class sc.fiji.snt.gui.cmds.mxOrganicLayoutPrefsCmd

Limit to the number of iterations that may take place.

maxIterations() - Method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Returns the value of the maxIterations record component.

maxPercentC() - Method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Returns the value of the maxPercentC record component.

maxPossibleRadius() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

maxRadius() - Method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Returns the value of the maxRadius record component.

maxSectionSize(int) - Method in class sc.fiji.snt.analysis.detection.PeripathDetector.Config

maxX - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

maxY - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

maxZ - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

mean() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCalibrator.CheckSummary

Returns the value of the mean record component.

mean() - Method in class sc.fiji.snt.analysis.RootAngleAnalyzer

MEAN - Enum constant in enum class sc.fiji.snt.analysis.ProfileProcessor.Metric

MEAN - Static variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D

Flag for integration of repeated measures: average

MEAN - Static variable in class sc.fiji.snt.analysis.ShollAnalyzer

MEAN_DIRECTION - Static variable in class sc.fiji.snt.analysis.RootAngleAnalyzer

MEAN_RADIUS - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics

Deprecated.

use #PATH_MEAN_RADIUS instead

MEAN_RADIUS - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Deprecated.

Use TreeStatistics.BRANCH_MEAN_RADIUS or TreeStatistics.PATH_MEAN_RADIUS instead

meanDirection() - Method in class sc.fiji.snt.analysis.RootAngleAnalyzer

Returns the mean direction of the fitted von Mises distribution.

meanGrowthRate() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalysisResults.GrowthSummaryStatistics

Returns the value of the meanGrowthRate record component.

meanRSquared() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalysisResults.GrowthSummaryStatistics

Returns the value of the meanRSquared record component.

meanTotalGrowth() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalysisResults.GrowthSummaryStatistics

Returns the value of the meanTotalGrowth record component.

measure(String, Collection<String>, boolean) - Method in class sc.fiji.snt.analysis.TreeStatistics

Measures this Tree, outputting the result to the measurements table.

measure(Collection<String>, boolean) - Method in class sc.fiji.snt.analysis.TreeStatistics

Measures this Tree, outputting the result to the measurements table using default row labels.

measureCells() - Method in class sc.fiji.snt.PathManagerUI

measureIndividualPaths(Collection<String>, boolean) - Method in class sc.fiji.snt.analysis.PathStatistics

Measures specified metrics for each individual path and creates a detailed table.

measurementsUnsaved() - Method in class sc.fiji.snt.PathManagerUI

measureOptions() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

measureQuick() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

MeasureUI - Class in sc.fiji.snt.gui

The MeasureUI class is a graphical user interface for measuring and analyzing Trees.

MeasureUI(Collection<Tree>) - Constructor for class sc.fiji.snt.gui.MeasureUI

MeasureUI(SNT, Collection<Tree>) - Constructor for class sc.fiji.snt.gui.MeasureUI

MEDIAN - Enum constant in enum class sc.fiji.snt.analysis.ProfileProcessor.Metric

MEDIAN - Enum constant in enum class sc.fiji.snt.SNT.FilterType

MEDIAN - Static variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D

Flag for integration of repeated measures: median

medianAngleDeg - Variable in class sc.fiji.snt.util.CrossoverFinder.CrossoverEvent

Median crossing angle between local tangents

medianMinDist - Variable in class sc.fiji.snt.util.CrossoverFinder.CrossoverEvent

Median segment-to-segment closest distance (real world units)

menuIcon(char, boolean) - Static method in class sc.fiji.snt.gui.IconFactory

menuIcon(char, boolean, Color) - Static method in class sc.fiji.snt.gui.IconFactory

menuIcon(IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory

menuIcon(IconFactory.GLYPH, Color) - Static method in class sc.fiji.snt.gui.IconFactory

menuItem(String, ActionListener, KeyStroke, char, boolean, Color) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

Creates a menu item with a right-aligned shortcut hint, an optional icon specified by a font symbol, and no global accelerator binding.

menuItem(String, ActionListener, KeyStroke, IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

Creates a menu item with a right-aligned shortcut hint, an optional icon, and no global accelerator binding.

menuItemTrigerringURL(String, String) - Static method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

menuItemTriggeringResources() - Static method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

menuKeyPressed(MenuKeyEvent) - Method in class sc.fiji.snt.gui.ScriptInstaller

menuKeyReleased(MenuKeyEvent) - Method in class sc.fiji.snt.gui.ScriptInstaller

menuKeyTyped(MenuKeyEvent) - Method in class sc.fiji.snt.gui.ScriptInstaller

merge(Collection<Tree>) - Static method in class sc.fiji.snt.util.TreeUtils

Combines all trees into a single Tree container.

merge(Tree) - Method in class sc.fiji.snt.Tree

Appends all paths of a specified Tree to this one.

MERGE - Static variable in class sc.fiji.snt.viewer.Annotation3D

mergeAnnotations(Collection<Annotation3D>, String) - Method in class sc.fiji.snt.viewer.Viewer3D

Merges a collection of annotations into a single object.

mergeContinuousPaths(Tree, double) - Static method in class sc.fiji.snt.util.TreeUtils

Merges paths that continue along the same trajectory at branch points, reducing fragmentation in auto-traced reconstructions.

mergePaths(List<Path>, boolean) - Static method in class sc.fiji.snt.util.TreeUtils

Merges a list of paths into a single path by appending nodes sequentially.

mergingDistance(double) - Method in class sc.fiji.snt.analysis.detection.AlongPathDetector.Config

Sets AlongPathDetector.Config.mergingDistance.

mergingDistance(double) - Method in class sc.fiji.snt.analysis.detection.LabelProximityDetector.Config

Sets the minimum distance between detections for NMS deduplication.

mergingDistance(double) - Method in class sc.fiji.snt.analysis.detection.PeripathDetector.Config

meshToDrawable(Mesh) - Static method in class sc.fiji.snt.viewer.Annotation3D

message() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCheck.Warning

Returns the value of the message record component.

metric - Variable in class sc.fiji.snt.Fill

metric - Variable in class sc.fiji.snt.gui.cmds.AnnotationGraphGeneratorCmd

metric - Variable in class sc.fiji.snt.gui.cmds.NewGraphOptionsCmd

MICROCHIP - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

micrometer() - Static method in class sc.fiji.snt.gui.GuiUtils

MIDPOINTS - Static variable in class sc.fiji.snt.PathFitter

Flag specifying that the computed path should only inherit midpoint refinement of node coordinates

min - Variable in class sc.fiji.snt.analysis.ColorMapper

min() - Method in class sc.fiji.snt.analysis.RootAngleAnalyzer

MIN - Enum constant in enum class sc.fiji.snt.analysis.ProfileProcessor.Metric

MIN_ANGLE_KEY - Static variable in class sc.fiji.snt.gui.cmds.PathFitterCmd

MIN_COST_PER_UNIT_DISTANCE - Static variable in class sc.fiji.snt.tracing.cost.DifferenceSq

MIN_COST_PER_UNIT_DISTANCE - Static variable in class sc.fiji.snt.tracing.cost.Reciprocal

MIN_INTENSITY_KEY - Static variable in class sc.fiji.snt.gui.cmds.MultiSpectralRefinerCmd

MIN_PERCENT - Static variable in class sc.fiji.snt.gui.GuiUtils.JTables.VisitingZoom

MIN_PERCENT_C_KEY - Static variable in class sc.fiji.snt.gui.cmds.MultiSpectralRefinerCmd

MIN_SNAP_CURSOR_WINDOW_XY - Static variable in class sc.fiji.snt.SNT

MIN_SNAP_CURSOR_WINDOW_Z - Static variable in class sc.fiji.snt.SNT

minBounds - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

minBranchIntensityLength - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

minIntensity - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

minIntensity(double) - Method in class sc.fiji.snt.analysis.detection.AlongPathDetector.Config

Sets AlongPathDetector.Config.minIntensity.

minIntensityThreshold() - Method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Returns the value of the minIntensityThreshold record component.

minPercentC() - Method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Returns the value of the minPercentC record component.

minRunNodes(int) - Method in class sc.fiji.snt.util.CrossoverFinder.Config

Sets CrossoverFinder.Config.minRunNodes.

minStepCost() - Method in interface sc.fiji.snt.tracing.cost.Cost

minStepCost() - Method in class sc.fiji.snt.tracing.cost.Difference

minStepCost() - Method in class sc.fiji.snt.tracing.cost.DifferenceSq

minStepCost() - Method in class sc.fiji.snt.tracing.cost.OneMinusErf

minStepCost() - Method in class sc.fiji.snt.tracing.cost.Reciprocal

MINUS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

minX - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

minY - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

minZ - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

MIP_OVERLAY_IDENTIFIER_PREFIX - Static variable in class sc.fiji.snt.hyperpanes.MultiDThreePanes

MLImporterCmd - Class in sc.fiji.snt.gui.cmds

Command for importing MouseLight reconstructions

MLImporterCmd() - Constructor for class sc.fiji.snt.gui.cmds.MLImporterCmd

MODE - Static variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D

Flag for integration of repeated measures: mode

modified - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor

Flag indicating whether the current graph has been modified

MOST_DISTAL - Static variable in class sc.fiji.snt.tracing.auto.BinaryTracer

Pruning mode: flag for most distal edge pruning (preserves proximal structure).

mouseDragged(MouseEvent) - Method in class sc.fiji.snt.gui.ComponentMover

Move the component to its new location.

mouseDragged(MouseEvent) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

MouseLightLoader - Class in sc.fiji.snt.io

Methods for retrieving reconstructions from MouseLight's online database at ml-neuronbrowser.janelia.org *

MouseLightLoader(String) - Constructor for class sc.fiji.snt.io.MouseLightLoader

Instantiates a new loader.

MouseLightQuerier - Class in sc.fiji.snt.io

Importer for retrieving reconstructions from MouseLight's online database at ml-neuronbrowser.janelia.org

mouseMovedTo(double, double, int, boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

mouseMovedTo(double, double, int, boolean) - Method in interface sc.fiji.snt.hyperpanes.PaneOwner

Called when the mouse is moved to a new position.

mouseMovedTo(double, double, int, boolean, boolean) - Method in class sc.fiji.snt.SNT

mousePressed(MouseEvent) - Method in class sc.fiji.snt.gui.ComponentMover

Setup the variables used to control the moving of the component:

mouseReleased(MouseEvent) - Method in class sc.fiji.snt.gui.ComponentMover

Restore the original state of the Component

MOVE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

moveNode(int, double, double, double) - Method in class sc.fiji.snt.Path

Assigns a new location to the specified node using raw coordinates.

moveNode(int, PointInImage) - Method in class sc.fiji.snt.Path

Assigns a new location to the specified node.

msg(String, String) - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

msg(String, String) - Method in class sc.fiji.snt.gui.cmds.ComputeSecondaryImg

muDeg() - Method in record class sc.fiji.snt.analysis.CircularModels.VonMisesFit

Returns the value of the muDeg record component.

MultiDThreePanes - Class in sc.fiji.snt.hyperpanes

Convenience class defining methods common to SNT's XY, XZ, and ZY panes

MultiDThreePanes() - Constructor for class sc.fiji.snt.hyperpanes.MultiDThreePanes

MultiDThreePanesCanvas - Class in sc.fiji.snt.hyperpanes

Canvas for displaying and interacting with multiple planes in 3D space, providing synchronized visualization and navigation across orthogonal projections.

MultiDThreePanesCanvas(ImagePlus, PaneOwner, int) - Constructor for class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

MultiPathTracerCanvas - Class in sc.fiji.snt

TracerCanvas variant that renders a caller-supplied collection of Paths: each in its own color, with one entry optionally "highlighted".

MultiPathTracerCanvas(ImagePlus, SNT, PathAndFillManager) - Constructor for class sc.fiji.snt.MultiPathTracerCanvas

Builds the canvas.

MultiPathTracerCanvas.Entry - Record Class in sc.fiji.snt

One painted path: the path itself, its base color, and whether to highlight it

multipleTreesExist() - Method in class sc.fiji.snt.PathAndFillManager

MultiSpectralRefiner - Class in sc.fiji.snt.analysis

Post-hoc refinement of traced paths in multispectral (e.g., Brainbow) images.

MultiSpectralRefiner(ImagePlus, Path) - Constructor for class sc.fiji.snt.analysis.MultiSpectralRefiner

Creates a refiner for a single path using an ImagePlus.

MultiSpectralRefiner(ImgPlus<T>, Path) - Constructor for class sc.fiji.snt.analysis.MultiSpectralRefiner

Creates a refiner for a single path using an ImgPlus.

MultiSpectralRefiner.Parameters - Record Class in sc.fiji.snt.analysis

Immutable parameter set for multispectral refinement.

MultiSpectralRefinerCmd - Class in sc.fiji.snt.gui.cmds

GUI command for MultiSpectralRefiner.

MultiSpectralRefinerCmd() - Constructor for class sc.fiji.snt.gui.cmds.MultiSpectralRefinerCmd

MultiSWCImporterCmd - Class in sc.fiji.snt.gui.cmds

Command for importing a folder of SWC files.

MultiSWCImporterCmd() - Constructor for class sc.fiji.snt.gui.cmds.MultiSWCImporterCmd

MultiTreeColorMapper - Class in sc.fiji.snt.analysis

Class for color coding groups of Trees.

MultiTreeColorMapper(Collection<Tree>) - Constructor for class sc.fiji.snt.analysis.MultiTreeColorMapper

Instantiates the MultiTreeColorMapper.

MultiTreeStatistics - Class in sc.fiji.snt.analysis

Computes summary and descriptive statistics from univariate properties of Tree groups.

MultiTreeStatistics(Collection<Tree>) - Constructor for class sc.fiji.snt.analysis.MultiTreeStatistics

Instantiates a new instance from a collection of Trees.

MultiTreeStatistics(Collection<Tree>, String...) - Constructor for class sc.fiji.snt.analysis.MultiTreeStatistics

Instantiates a new instance from a collection of Trees.

MultiViewer2D - Class in sc.fiji.snt.viewer

Class for rendering montages of Trees as 2D plots that can be exported as SVG, PNG or PDF.

MultiViewer2D(Collection<Tree>) - Constructor for class sc.fiji.snt.viewer.MultiViewer2D

MultiViewer2D(List<Viewer2D>) - Constructor for class sc.fiji.snt.viewer.MultiViewer2D

MultiViewer3D - Class in sc.fiji.snt.viewer

Class for rendering individual Viewer3Ds as a multi-panel montage.

MultiViewer3D(Collection<Tree>) - Constructor for class sc.fiji.snt.viewer.MultiViewer3D

Assembles a multi-panel viewer from a list of trees (1 per panel)

MultiViewer3D(List<Viewer3D>) - Constructor for class sc.fiji.snt.viewer.MultiViewer3D

Assembles a multi-panel viewer from a list of viewers (1 per panel)

mxCircleLayoutGrouped - Class in sc.fiji.snt.viewer.geditor

Circle layout algorithm for grouped annotation graph visualization.

mxCircleLayoutGrouped(mxGraph, int, int) - Constructor for class sc.fiji.snt.viewer.geditor.mxCircleLayoutGrouped

mxCircleLayoutGroupedCmd - Class in sc.fiji.snt.gui.cmds

SciJava Command implementing grouped circular layout algorithm for graph visualization with multi-level organizational hierarchy support.

mxCircleLayoutGroupedCmd() - Constructor for class sc.fiji.snt.gui.cmds.mxCircleLayoutGroupedCmd

mxCircleLayoutScaled - Class in sc.fiji.snt.viewer.geditor

A circle layout that is more compact than the default mxCircleLayout by applying a 'reduction factor' to the layout radius.

mxCircleLayoutScaled(mxGraph) - Constructor for class sc.fiji.snt.viewer.geditor.mxCircleLayoutScaled

mxCircleLayoutSorted - Class in sc.fiji.snt.viewer.geditor

Sorted circle layout algorithm for SNT graphs.

mxCircleLayoutSorted(mxGraph, String) - Constructor for class sc.fiji.snt.viewer.geditor.mxCircleLayoutSorted

mxOrganicLayoutPrefsCmd - Class in sc.fiji.snt.gui.cmds

Command for setting parameters of the mxOrganicLayout Graph layout used in GraphEditor.

mxOrganicLayoutPrefsCmd() - Constructor for class sc.fiji.snt.gui.cmds.mxOrganicLayoutPrefsCmd

myOffScreenX(int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Converts a screen x-coordinate to an offscreen (image) x-coordinate.

myOffScreenXD(int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Converts a screen x-coordinate to a floating-point offscreen (image) x-coordinate.

myOffScreenY(int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Converts a screen y-coordinate to an offscreen (image) y-coordinate.

myOffScreenYD(int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Converts a screen y-coordinate to a floating-point offscreen (image) y-coordinate.

myScreenX(int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Converts an offscreen (image) x-coordinate to a screen x-coordinate.

myScreenXD(double) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Converts a floating-point offscreen (image) x-coordinate to a screen x-coordinate.

myScreenXDprecise(double) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Converts an offscreen (image) x-coordinate to a screen x-coordinate with floating-point precision.

myScreenY(int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Converts an offscreen (image) y-coordinate to a screen y-coordinate.

myScreenYD(double) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Converts a floating-point offscreen (image) x-coordinate to a screen x-coordinate.

myScreenYDprecise(double) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Converts an offscreen (image) y-coordinate to a screen y-coordinate with floating-point precision.

N

N_BRANCH_NODES - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "No. of branch nodes (branch fragmentation)"

N_BRANCH_POINTS - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: No. of branch points

N_BRANCH_POINTS - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "No. of branch points"

N_BRANCHES - Static variable in class sc.fiji.snt.analysis.MultiTreeColorMapper

Mapping property: Count of all branches

N_BRANCHES - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "No. of branches"

N_CHILDREN - Static variable in class sc.fiji.snt.analysis.PathStatistics

Flag for "No. of children" analysis.

N_FITTED_PATHS - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "No. of fitted paths"

N_INNER_BRANCHES - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "No. of inner branches"

N_MAX - Static variable in class sc.fiji.snt.analysis.ShollAnalyzer

N_NODES - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: No. of nodes

N_NODES - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "No. of nodes"

N_PATH_NODES - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "No. of path nodes (path fragmentation)"

N_PATHS - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "No. of paths"

N_PRIMARY_BRANCHES - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "No. of primary branches"

N_SECONDARY_MAX - Static variable in class sc.fiji.snt.analysis.ShollAnalyzer

N_SPINES - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: No. of spines/varicosities

N_SPINES - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "No. of spines/varicosities"

N_TERMINAL_BRANCHES - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "No. of terminal branches"

N_TIPS - Static variable in class sc.fiji.snt.analysis.MultiTreeColorMapper

Mapping property: Count of all tips (end points)

N_TIPS - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "No. of tips"

name() - Method in class sc.fiji.snt.annotation.AllenCompartment

name() - Method in interface sc.fiji.snt.annotation.BrainAnnotation

Returns the compartment's name.

name() - Method in class sc.fiji.snt.annotation.DrosophilaCompartment

name() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

NAVIGATE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

NBASTAR - Enum constant in enum class sc.fiji.snt.SNT.SearchType

NDFImporter - Class in sc.fiji.snt.io

Importer for NeuronJ data files.

NDFImporter(File) - Constructor for class sc.fiji.snt.io.NDFImporter

NDFImporter(InputStream) - Constructor for class sc.fiji.snt.io.NDFImporter

NDFImporter(String) - Constructor for class sc.fiji.snt.io.NDFImporter

NDFImporterCmd - Class in sc.fiji.snt.gui.cmds

Command for importing a NeuronJ NDF file.

NDFImporterCmd() - Constructor for class sc.fiji.snt.gui.cmds.NDFImporterCmd

nDimensions() - Method in class sc.fiji.snt.analysis.sholl.Profile

near - Variable in class sc.fiji.snt.NearPoint

nearClip - Variable in class sc.fiji.snt.viewer.Bvv.Keyframe

Near clipping distance (slab front).

nearest(double, double, double, double) - Method in class sc.fiji.snt.seed.SeedOverlay

Returns the seed closest to (x, y, z) in physical units, or null if the overlay is empty or no seed lies within maxDistance.

NEAREST_NEIGHBOR_DISTANCE - Static variable in class sc.fiji.snt.analysis.NodeColorMapper

Flag for "Nearest neighbor distance" statistics.

NEAREST_NEIGHBOR_DISTANCE - Static variable in class sc.fiji.snt.analysis.NodeStatistics

Flag for "Nearest neighbor distance" statistics.

nearestNodeTo(PointInImage, double) - Method in class sc.fiji.snt.Path

Gets the closest node associated with the specified node.

nearestPointOnAnyPath(double, double, double, double) - Method in class sc.fiji.snt.PathAndFillManager

nearestPointOnAnyPath(Collection<Path>, PointInCanvas, double) - Method in class sc.fiji.snt.PathAndFillManager

nearestPointOnAnyPath(Collection<Path>, PointInImage, double, boolean) - Method in class sc.fiji.snt.PathAndFillManager

NearPoint - Class in sc.fiji.snt

This class encapsulates the relationship between an arbitrary point (nearPoint.x,nearPoint.y,nearPoint.z) close to a particular point on a particular path.

NearPoint(PointInImage, Path, int) - Constructor for class sc.fiji.snt.NearPoint

NearPoint(PointInImage, Path, int, boolean) - Constructor for class sc.fiji.snt.NearPoint

negative() - Method in record class sc.fiji.snt.analysis.curation.CurationTags.Partition

Returns the value of the negative record component.

NEGATIVE - Static variable in class sc.fiji.snt.analysis.curation.CurationTags

Tag value applied to paths rejected during review.

neighborDistances - Variable in class sc.fiji.snt.tracing.AbstractSearch

neuriteCount() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalysisResults.GrowthSummaryStatistics

Returns the value of the neuriteCount record component.

NeuriteGrowthData - Class in sc.fiji.snt.analysis.growth

Data container for growth analysis results of a single neurite over time.

NeuriteGrowthData(String) - Constructor for class sc.fiji.snt.analysis.growth.NeuriteGrowthData

Creates a new NeuriteGrowthData container for the specified neurite.

NeurolucidaImporter - Class in sc.fiji.snt.io

Importer for Neurolucida XML files (Neuromorphological File Specification / NMF format).

NeurolucidaImporter(File) - Constructor for class sc.fiji.snt.io.NeurolucidaImporter

Creates a new importer from a File.

NeurolucidaImporter(InputStream) - Constructor for class sc.fiji.snt.io.NeurolucidaImporter

Creates a new importer from an InputStream.

NeurolucidaImporter(String) - Constructor for class sc.fiji.snt.io.NeurolucidaImporter

Creates a new importer from a file path.

NeuroMorphoLoader - Class in sc.fiji.snt.io

Importer for retrieving SWC data from neuromorpho.org.

NeuroMorphoLoader() - Constructor for class sc.fiji.snt.io.NeuroMorphoLoader

NewGraphOptionsCmd - Class in sc.fiji.snt.gui.cmds

GUI for "New Graph Options" Command

NewGraphOptionsCmd() - Constructor for class sc.fiji.snt.gui.cmds.NewGraphOptionsCmd

newRecViewer(boolean) - Method in class sc.fiji.snt.SNTService

Instantiates a new standalone Reconstruction Viewer.

newScript(String, String) - Static method in class sc.fiji.snt.gui.ScriptInstaller

newSlice(int) - Method in class sc.fiji.snt.tracing.image.SearchImageStack

NEWSPAPER - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

next() - Method in class sc.fiji.snt.PathAndFillManager.AllPointsIterator

next() - Method in class sc.fiji.snt.util.CircleCursor3D

next() - Method in class sc.fiji.snt.util.PathCursor

NEXT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

nextZoomLevel(double) - Static method in class sc.fiji.snt.util.ImpUtils

NO_EVENT - Static variable in class sc.fiji.snt.event.SNTEvent

Event type indicating no specific event

NO_IMAGE_ASSOCIATED_DATA - Static variable in class sc.fiji.snt.SNTPrefs

Node() - Constructor for class sc.fiji.snt.Fill.Node

NODE_RADIUS - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Node radius

NODE_RADIUS - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Node radius"

NodeColorMapper - Class in sc.fiji.snt.analysis

Class for color coding of NodeStatistics results.

NodeColorMapper(NodeStatistics<?>) - Constructor for class sc.fiji.snt.analysis.NodeColorMapper

Instantiates the mapper.

NodeColorMapper(NodeStatistics<?>, Context) - Constructor for class sc.fiji.snt.analysis.NodeColorMapper

Instantiates the mapper.

nodeDiameter() - Method in class sc.fiji.snt.TracerCanvas

Returns the diameter of path nodes rendered at current magnification.

nodeDistributionCostFactor - Variable in class sc.fiji.snt.gui.cmds.mxOrganicLayoutPrefsCmd

Cost factor applied to energy calculations involving the general node distribution of the graph.

nodeIcon(Color) - Static method in class sc.fiji.snt.gui.IconFactory

nodeIcon(Color, boolean, boolean) - Static method in class sc.fiji.snt.gui.IconFactory

nodeIconMulticolor(boolean, boolean) - Static method in class sc.fiji.snt.gui.IconFactory

nodeIndex - Variable in class sc.fiji.snt.analysis.detection.Detection

Index of the nearest node on the associated path

NodeProfiler - Class in sc.fiji.snt.analysis

Command to retrieve node profiles (plots of voxel intensities sampled across Path nodes).

NodeProfiler() - Constructor for class sc.fiji.snt.analysis.NodeProfiler

Empty constructor used by CommandService before calling NodeProfiler.run().

NodeProfiler(Dataset) - Constructor for class sc.fiji.snt.analysis.NodeProfiler

Instantiates a new Profiler.

nodes_as_image - Variable in class sc.fiji.snt.tracing.BiSearch

nodes_as_image_from_goal - Variable in class sc.fiji.snt.tracing.SearchThread

nodes_as_image_from_start - Variable in class sc.fiji.snt.tracing.SearchThread

NodeStatistics<T> - Class in sc.fiji.snt.analysis

Computes summary and descriptive statistics from a Collection of nodes, including convenience methods to plot distributions of such data.

NodeStatistics(Collection<T>) - Constructor for class sc.fiji.snt.analysis.NodeStatistics

Performs statistics on a collection of nodes.

NodeStatistics(Collection<T>, Tree) - Constructor for class sc.fiji.snt.analysis.NodeStatistics

Performs statistics on a collection of nodes.

nodeToPixelCoords(PointInImage, double, double, double) - Static method in class sc.fiji.snt.filter.SpectralSimilarity

Converts a path node from calibrated (real-world) coordinates to pixel coordinates by dividing by the voxel spacing and rounding.

nodeToVoxelPos(SWCPoint, long[]) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Converts an SWCPoint's physical coordinates to voxel position.

nodeWitnessRadius - Variable in class sc.fiji.snt.util.CrossoverFinder.Config

Radius (in real‑world units) used by the post‑hoc witness filter.

nodeWitnessRadius(double) - Method in class sc.fiji.snt.util.CrossoverFinder.Config

Sets CrossoverFinder.Config.nodeWitnessRadius.

noImgError() - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

noMoreThanOneEvery - Static variable in class sc.fiji.snt.Path

Deprecated.

Use Path.DEFAULT_SAMPLING_INTERVAL instead

NON_DEMO_SCRIPT - Static variable in class sc.fiji.snt.gui.ScriptInstaller

Pattern to match non-demo scripts (case-insensitive)

nonDraggableRightSplitPane() - Static method in class sc.fiji.snt.gui.GuiUtils.SplitPanes

NONE - Enum constant in enum class sc.fiji.snt.analysis.ProfileProcessor.Shape

NONE - Static variable in class sc.fiji.snt.analysis.PathProfiler

noPathsError() - Method in class sc.fiji.snt.SNTUI

norm180(double) - Static method in class sc.fiji.snt.analysis.CircularModels

Normalizes deg to [0,180[

norm360(double) - Static method in class sc.fiji.snt.analysis.CircularModels

Normalizes deg to [0,360).

NormalizedProfileStats - Class in sc.fiji.snt.analysis.sholl.math

Calculates Sholl Metrics from normalized profiles, including Sholl decay and methods for determination of 'optimal' normalization.

NormalizedProfileStats(Profile, int) - Constructor for class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

NormalizedProfileStats(Profile, int, int) - Constructor for class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

NormalizedProfileStats(Profile, ShollStats.DataMode, int) - Constructor for class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

NormalizedProfileStats(Profile, ShollStats.DataMode, int, int) - Constructor for class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

normalizeVector(double[]) - Static method in class sc.fiji.snt.filter.SpectralSimilarity

Normalizes a vector to unit length in place.

normalSideOfPlane(double, double, double, double, double, double, double, double, double) - Static method in class sc.fiji.snt.NearPoint

NotesUI - Class in sc.fiji.snt

Implements the Notepad pane.

NotesUI(SNTUI) - Constructor for class sc.fiji.snt.NotesUI

Constructs a Notepad instance.

notify(String, int) - Static method in class sc.fiji.snt.gui.GuiUtils

Displays a floating notification in the upper corner of the active screen

notifyExternalDataLoaded() - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

notifyIfNewVersion(int) - Method in class sc.fiji.snt.gui.GuiUtils

notifyIfOldVersion(int) - Method in class sc.fiji.snt.gui.GuiUtils

Checks for available SNT updates in the background by querying the Neuroanatomy update site.

notifyListeners(SNTEvent) - Method in class sc.fiji.snt.SNT

notifyLoadingEnd(Viewer3D) - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

notifyLoadingStart(Viewer3D) - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

noValidImageDataError() - Method in class sc.fiji.snt.SNTUI

noValidImgError() - Method in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

nPoints - Variable in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

nPoints - Variable in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

numDimensions() - Method in class sc.fiji.snt.util.CircleCursor3D

numDimensions() - Method in class sc.fiji.snt.util.PathCursor

O

OBJMesh - Class in sc.fiji.snt.viewer

An OBJMesh stores information about a Wavefront .obj mesh loaded into Viewer3D, with access points to its OBJFile and DrawableVBO

OBJMesh(String) - Constructor for class sc.fiji.snt.viewer.OBJMesh

Instantiates a new wavefront OBJ mesh from a file path/URL.

OBJMesh(URL, String) - Constructor for class sc.fiji.snt.viewer.OBJMesh

odc() - Method in record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.Report

Returns the value of the odc record component.

of(Number[]) - Static method in interface sc.fiji.snt.util.SNTPoint

of(Number, Number, Number) - Static method in interface sc.fiji.snt.util.SNTPoint

Script friendly method for instantiating a new point.

OmeAxisUtils - Class in sc.fiji.snt.io

Utility for setting ImgPlus axes from OME metadata (OME-XML or OME-Zarr).

OmeAxisUtils() - Constructor for class sc.fiji.snt.io.OmeAxisUtils

OmeAxisUtils.OmeMetadata - Record Class in sc.fiji.snt.io

Parsed OME metadata container.

OmeMetadata(String, Map<String, Long>, Map<String, Double>, Map<String, String>, String) - Constructor for record class sc.fiji.snt.io.OmeAxisUtils.OmeMetadata

Creates an instance of a OmeMetadata record class.

OneMinusErf - Class in sc.fiji.snt.tracing.cost

A cost function inspired by an A* search implementation in the Janelia Workstation, where the cost of moving to a new voxel is given by the complementary error function 1 - erf(z), where

OneMinusErf(double, double, double) - Constructor for class sc.fiji.snt.tracing.cost.OneMinusErf

oneMinusErfZFudge - Variable in class sc.fiji.snt.SNT

onEvent(DataDeletedEvent) - Method in class sc.fiji.snt.plugin.ShollAnalysisImgInteractiveCmd

onEvent(SNTEvent) - Method in interface sc.fiji.snt.event.SNTListener

Called when an SNT event occurs.

onForkInitiated(Path, int) - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

Hook 1: Fork initiation. Called from SNT.startPath() when the user Alt-clicks to start a branch.

onNodeEdited(Path, int) - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

Hook 4: Node editing. Called after a node is moved, inserted, or deleted during edit mode.

onPath - Variable in class sc.fiji.snt.util.PointInImage

The Path associated with this node, if any (optional field)

onPathFinalized(Path) - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

Hook 3: Path finalization. Called when the user completes an entire path (SNT.finishPath()).

onSegmentCompleted(Path) - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

Hook 2: Segment completion. Called from SNT.searchFinished() when A* returns a candidate segment, before the user sees the keep/junk dialog.

OntologyBrowser - Class in sc.fiji.snt.gui

A reusable panel that presents one or more hierarchical ontologies as searchable checkbox trees.

OntologyBrowser() - Constructor for class sc.fiji.snt.gui.OntologyBrowser

Creates an empty OntologyBrowser with multi-selection enabled.

OntologyBrowser(boolean) - Constructor for class sc.fiji.snt.gui.OntologyBrowser

Creates an empty OntologyBrowser.

OntologyBrowser.AllenCCFRenderer - Class in sc.fiji.snt.gui

Default cell renderer for Allen CCF ontology trees.

OntologyBrowser.OntologyTab - Class in sc.fiji.snt.gui

Represents a single ontology tab containing a searchable checkbox tree.

oofFile - Variable in class sc.fiji.snt.tracing.TubularGeodesicsTracer

open - Variable in class sc.fiji.snt.Fill.Node

open(ImagePlus...) - Static method in class sc.fiji.snt.viewer.Bvv

Convenience factory: creates a standalone BVV viewer and displays one or more ImagePlus volumes in one step.

open(File) - Static method in class sc.fiji.snt.util.ImgUtils

Opens an image file as an ImgPlus.

open(File) - Static method in class sc.fiji.snt.util.ImpUtils

open(File, String) - Static method in class sc.fiji.snt.util.ImpUtils

open(String) - Static method in class sc.fiji.snt.util.ImgUtils

Opens an image file using SCIFIO, supporting lazy loading for large formats.

open(String) - Static method in class sc.fiji.snt.util.ImpUtils

open(String) - Static method in class sc.fiji.snt.viewer.Bvv

Convenience factory: opens a file path into a BVV viewer.

open(String...) - Static method in class sc.fiji.snt.viewer.Bvv

Convenience factory: opens one or more file paths into the same BVV viewer window, choosing the most appropriate loading strategy per file: .ims Imaris HDF5: creates a BDV XML sidecar file next to the .ims file (using the same base name, e.g.

open(String, String) - Static method in class sc.fiji.snt.util.ImpUtils

open(List<?>) - Static method in class sc.fiji.snt.viewer.Bvv

Script friendly convenience factory: creates a standalone BVV viewer and displays a list of images in one step.

open(AbstractSpimData<?>) - Static method in class sc.fiji.snt.viewer.Bvv

Convenience factory: creates a standalone BVV viewer and displays a AbstractSpimData dataset using BVV's pyramid-aware GPU cache manager.

open(ImgPlus<T>...) - Static method in class sc.fiji.snt.viewer.Bvv

Convenience factory: creates a standalone BVV viewer and displays one or more ImgPlus volumes in one step.

open(SNT) - Static method in class sc.fiji.snt.viewer.Bvv

Convenience factory: creates a BVV instance tethered to the given SNT instance and immediately displays its currently loaded image data.

OPEN - Enum constant in enum class sc.fiji.snt.tracing.BiSearchNode.State

OPEN_DIALOG - Static variable in class sc.fiji.snt.gui.FilePicker

OPEN_FOLDER - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

open_from_goal - Variable in class sc.fiji.snt.tracing.BiSearch

OPEN_FROM_GOAL - Static variable in class sc.fiji.snt.tracing.SearchThread

open_from_start - Variable in class sc.fiji.snt.tracing.BiSearch

open_from_start - Variable in class sc.fiji.snt.tracing.SearchThread

OPEN_FROM_START - Static variable in class sc.fiji.snt.tracing.SearchThread

openCharts() - Static method in class sc.fiji.snt.analysis.SNTChart

OpenDatasetCmd - Class in sc.fiji.snt.gui.cmds

Implements the 'Choose Tracing Image (From File)...' command.

OpenDatasetCmd() - Constructor for class sc.fiji.snt.gui.cmds.OpenDatasetCmd

openFile(String) - Method in class sc.fiji.snt.SNTUI

openHelpURL(String, String) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

openReconstructionFile(String) - Method in class sc.fiji.snt.SNTUI

openScript(String, String) - Method in class sc.fiji.snt.gui.ScriptInstaller

openURL(String) - Static method in class sc.fiji.snt.gui.GuiUtils

openURL(String, String) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

ops - Variable in class sc.fiji.snt.io.WekaModelLoader

opService - Variable in class sc.fiji.snt.analysis.AbstractConvexHull

options() - Static method in class sc.fiji.snt.gui.GuiUtils.Buttons

OPTIONS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

OPTIONS_MENU - Static variable in class sc.fiji.snt.gui.SearchField

optionsButton() - Method in class sc.fiji.snt.gui.SearchField

optionsButton(JPopupMenu) - Method in class sc.fiji.snt.gui.SNTEditorPane

OptionsButton(IconFactory.GLYPH, float, JPopupMenu) - Static method in class sc.fiji.snt.gui.GuiUtils.Buttons

orderByEndpointProximity(Collection<Path>) - Static method in class sc.fiji.snt.util.TreeUtils

Orders a collection of paths to form a spatially continuous chain based on endpoint proximity.

orientationPeaks() - Method in record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.Report

Returns the value of the orientationPeaks record component.

orientPathsForMerging(List<Path>) - Static method in class sc.fiji.snt.util.TreeUtils

Orients paths in a chain so they can be merged end-to-start.

orientPathsTowardRoot(Collection<Path>, PointInImage) - Static method in class sc.fiji.snt.util.TreeUtils

Orients paths so their start nodes point toward a given root location.

orientTowardDirection(PCAnalyzer.PrincipalAxis[], double[]) - Static method in class sc.fiji.snt.analysis.PCAnalyzer

Orients principal axes so the primary axis points toward a reference direction, i.e., the primary axis is oriented to minimize the angle with the reference direction.

orientTowardTips(PCAnalyzer.PrincipalAxis[], Tree) - Static method in class sc.fiji.snt.analysis.PCAnalyzer

Convenience method to orient existing principal axes toward a tree's tips centroid.

origin - Variable in class sc.fiji.snt.util.BoundingBox

The bounding box origin (SE, lower corner)

origin() - Method in class sc.fiji.snt.util.BoundingBox

Retrieves the origin of this box.

originalImgChoice - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

originOpposite - Variable in class sc.fiji.snt.util.BoundingBox

The origin opposite (NW, upper corner)

originOpposite() - Method in class sc.fiji.snt.util.BoundingBox

Retrieves the origin opposite of this box.

OUT_DEGREE - Static variable in class sc.fiji.snt.analysis.graph.GraphColorMapper

Flag for "Out degree" mapping.

OUT_OF_MEMORY - Static variable in class sc.fiji.snt.tracing.SearchThread

outerRadius(double) - Method in class sc.fiji.snt.analysis.detection.PeripathDetector.Config

outerRadiusMultiplier(double) - Method in class sc.fiji.snt.analysis.detection.PeripathDetector.Config

OUTGOING_WEIGHT - Static variable in class sc.fiji.snt.analysis.graph.GraphColorMapper

Flag for "Outgoing weight" mapping.

outOfBounds(long[], long[], long[]) - Static method in class sc.fiji.snt.util.ImgUtils

Checks if pos is outside the bounds given by min and max

OUTPUT_CIRCLE - Static variable in class sc.fiji.snt.tracing.auto.SomaUtils

Output type: Circular ROI with estimated radius

OUTPUT_CONTOUR - Static variable in class sc.fiji.snt.tracing.auto.SomaUtils

Output type: Area ROI from flood fill contour

OUTPUT_POINT - Static variable in class sc.fiji.snt.tracing.auto.SomaUtils

Output type: Point ROI at soma center

overlayShells() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCommonCmd

overshootRemovalEnabled - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

owner - Variable in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

P

p1AtStart() - Method in record class sc.fiji.snt.util.TreeUtils.EndpointMatch

Returns the value of the p1AtStart record component.

p2AtStart() - Method in record class sc.fiji.snt.util.TreeUtils.EndpointMatch

Returns the value of the p2AtStart record component.

Package Organization - Search tag in package sc.fiji.snt.tracing

Section

PAGE_RANK - Static variable in class sc.fiji.snt.analysis.graph.GraphColorMapper

Flag for "Page rank" mapping.

paint(Graphics) - Method in class sc.fiji.snt.TracerCanvas

paintAnnulus(RandomAccessibleInterval<T>, int, double, double, double, double, double[], double[], double, double, double, double, double, double) - Static method in class sc.fiji.snt.tracing.CrossSectionUtils

Paints an annular cross-section into a 3D output image.

paletteDismissed() - Method in class sc.fiji.snt.gui.cmds.ComputeSecondaryImg

paletteDismissed() - Method in interface sc.fiji.snt.gui.SigmaPaletteListener

paletteDisplayed() - Method in class sc.fiji.snt.gui.cmds.ComputeSecondaryImg

paletteDisplayed() - Method in interface sc.fiji.snt.gui.SigmaPaletteListener

PaletteOptions - Class in sc.fiji.snt.gui

Per-palette delegate that builds the "More »" pop-up menu and supplies supporting operations (LUT, MIP overlay, snapshot, etc.) shared by SNT's preview-wizard windows (SigmaPalette, and CostPalette).

PaletteOptions(ImagePlus, ImagePlus, String, Runnable) - Constructor for class sc.fiji.snt.gui.PaletteOptions

PaneOwner - Interface in sc.fiji.snt.hyperpanes

Interface for objects that own and manage multi-pane displays, handling mouse interactions, zoom events, and pan events across multiple viewing planes.

panEventOccurred(int, int, int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

panEventOccurred(int, int, int) - Method in interface sc.fiji.snt.hyperpanes.PaneOwner

Called when a pan event occurs.

panMode - Variable in class sc.fiji.snt.SNT

parallelBranchPruneEnabled - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Parameters(double, double, double, double, double, double, double, double, double, int, int, double, int, boolean) - Constructor for record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Creates an instance of a Parameters record class.

paramLabel() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCalibrator.CheckSummary

Returns the value of the paramLabel record component.

parent - Variable in class sc.fiji.snt.util.SWCPoint

The parent id of this node

parentPath - Variable in class sc.fiji.snt.Path

parse() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

parse() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D

parse() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser3D

parse() - Method in interface sc.fiji.snt.analysis.sholl.parsers.Parser

Performs the parsing operation to extract the Sholl profile.

parse() - Method in class sc.fiji.snt.analysis.sholl.parsers.TabularParser

Parses the tabular data to extract the Sholl profile.

parse() - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

parseOmeXml(String) - Static method in class sc.fiji.snt.io.OmeAxisUtils

Parse OME-XML metadata file.

parseOmeXmlString(String) - Static method in class sc.fiji.snt.io.OmeAxisUtils

Parse OME-XML from string content (for remote files).

parseOmeZarrAttrs(String) - Static method in class sc.fiji.snt.io.OmeAxisUtils

Parse OME-Zarr .zattrs file (level 0).

parseOmeZarrAttrs(String, int) - Static method in class sc.fiji.snt.io.OmeAxisUtils

Parse OME-Zarr .zattrs file at specific level.

parseOmeZarrAttrsString(String) - Static method in class sc.fiji.snt.io.OmeAxisUtils

Parse OME-Zarr .zattrs from string content (level 0).

parseOmeZarrAttrsString(String, int) - Static method in class sc.fiji.snt.io.OmeAxisUtils

Parse OME-Zarr .zattrs from string content at specific resolution level.

Parser - Interface in sc.fiji.snt.analysis.sholl.parsers

Interface for parsing data sources to extract Sholl analysis profiles.

participants - Variable in class sc.fiji.snt.util.CrossoverFinder.CrossoverEvent

Unique paths taking part in the crossover

Partition(List<Path>, List<Path>, List<Path>, List<Path>) - Constructor for record class sc.fiji.snt.analysis.curation.CurationTags.Partition

Creates an instance of a Partition record class.

PARTITION_ASYMMETRY - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Partition asymmetry"

partitionByReviewStatus(Collection<Path>) - Static method in class sc.fiji.snt.analysis.curation.CurationTags

Sibling of CurationTags.partitionByReviewStatus(Tree) that accepts any iterable of paths.

partitionByReviewStatus(Tree) - Static method in class sc.fiji.snt.analysis.curation.CurationTags

Splits a Tree's paths into four buckets by review status: positive, negative, unsure, and unreviewed (no cur:* tag).

partsNearbyCSpinner - Variable in class sc.fiji.snt.SNTUI

PASTE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

patchImsXml(String, String) - Static method in class sc.fiji.snt.io.SpimDataUtils

Patches an IMS XML sidecar file, replacing all "(name not specified)" placeholders with sequential channel names derived from the base name.

path - Variable in class sc.fiji.snt.analysis.detection.Detection

The path this detection is associated with

path() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.TimePoint

Returns the value of the path record component.

path() - Method in record class sc.fiji.snt.MultiPathTracerCanvas.Entry

Returns the value of the path record component.

Path - Class in sc.fiji.snt

This class represents a traced segment (i.e., a Path) in a reconstruction.

Path() - Constructor for class sc.fiji.snt.Path

Instantiates a new path under default settings (isotropic 1um pixel spacing)

Path(double, double, double, String) - Constructor for class sc.fiji.snt.Path

Instantiates a new path.

PATH_AVG_SPINE_DENSITY - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Path spine/varicosity density

PATH_CHANNEL - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Path channel"

PATH_CONTRACTION - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Path contraction"

PATH_DISTANCE - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Path distance to soma

PATH_EXT_ANGLE - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Path's extension angle

PATH_EXT_ANGLE - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Path extension angle"

PATH_EXT_ANGLE_REL - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Path's extension angle (Rel.)

PATH_EXT_ANGLE_REL - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Path extension angle (Rel.)"

PATH_EXT_ANGLE_XY - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Path's extension angle (XY plane)

PATH_EXT_ANGLE_XY - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Path extension angle XY"

PATH_EXT_ANGLE_XZ - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Path's extension angle (XZ plane)

PATH_EXT_ANGLE_XZ - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Path extension angle XZ"

PATH_EXT_ANGLE_ZY - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Path's extension angle (ZY plane)

PATH_EXT_ANGLE_ZY - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Path extension angle ZY"

PATH_FRACTAL_DIMENSION - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Path fractal dimension"

PATH_FRAME - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Path frame

PATH_FRAME - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Path frame"

PATH_LENGTH - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Path length

PATH_LENGTH - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Path length"

PATH_MEAN_RADIUS - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Path mean radius

PATH_MEAN_RADIUS - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Path mean radius"

PATH_N_SPINES - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "No. of spines/varicosities per path"

PATH_ORDER - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Path order

PATH_ORDER - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Path order"

PATH_SPINE_DENSITY - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Path spine/varicosity density"

PATH_SURFACE_AREA - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying Path surface area statistics.

PATH_VOLUME - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying Path volume statistics.

Path.PathNode - Class in sc.fiji.snt

Enhanced PointInImage that stores all node-specific properties.

PathAnalyzerCmd - Class in sc.fiji.snt.plugin

Command for measuring Paths in isolation.

PathAnalyzerCmd() - Constructor for class sc.fiji.snt.plugin.PathAnalyzerCmd

pathAndFillManager - Variable in class sc.fiji.snt.TracerCanvas

PathAndFillManager - Class in sc.fiji.snt

The PathAndFillManager is responsible for importing, handling and managing of Paths and Fills.

PathAndFillManager() - Constructor for class sc.fiji.snt.PathAndFillManager

Instantiates a new PathAndFillManager using default values.

PathAndFillManager(double, double, double, String) - Constructor for class sc.fiji.snt.PathAndFillManager

Instantiates a new PathAndFillManager imposing specified pixel dimensions, which may be required for pixel operations.

PathAndFillManager(SNT) - Constructor for class sc.fiji.snt.PathAndFillManager

PathAndFillManager.AllPointsIterator - Class in sc.fiji.snt

pathChanged(PathChangeEvent) - Method in class sc.fiji.snt.PathAndFillManager

PathCursor<T> - Class in sc.fiji.snt.util

Iterate over the pixels along the defined nodes of a Path

PathCursor(RandomAccessible<T>, Path) - Constructor for class sc.fiji.snt.util.PathCursor

PathDownsampler - Class in sc.fiji.snt

This is an implementation of the Ramer-Douglas-Peucker algorithm for simplifying a curve represented by line-segments, as described here

PathDownsampler() - Constructor for class sc.fiji.snt.PathDownsampler

PathFitter - Class in sc.fiji.snt

Class for fitting circular cross-sections around existing nodes of a Path in order to compute radii (node thickness) and midpoint refinement of existing coordinates.

PathFitter(ImagePlus, Path) - Constructor for class sc.fiji.snt.PathFitter

Instantiates a new PathFitter.

PathFitter(ImgPlus<? extends RealType<?>>, Path) - Constructor for class sc.fiji.snt.PathFitter

Instantiates a new PathFitter.

PathFitter(RandomAccessibleInterval<? extends RealType<?>>, Path, double, double, double, String) - Constructor for class sc.fiji.snt.PathFitter

Instantiates a new PathFitter directly from pixel data.

PathFitter(SNT, Path) - Constructor for class sc.fiji.snt.PathFitter

Instantiates a new PathFitter.

PathFitterCmd - Class in sc.fiji.snt.gui.cmds

GUI command for PathFitter

PathFitterCmd() - Constructor for class sc.fiji.snt.gui.cmds.PathFitterCmd

PathManagerUI - Class in sc.fiji.snt

Implements the Path Manager Dialog.

PathManagerUI(SNT) - Constructor for class sc.fiji.snt.PathManagerUI

Instantiates a new Path Manager Dialog.

PathManagerUISearchableBar - Class in sc.fiji.snt.gui

Implements the customized SearchableBar used by PathManagerUI, including GUI commands for selection and morphological filtering of Paths.

PathManagerUISearchableBar(PathManagerUI) - Constructor for class sc.fiji.snt.gui.PathManagerUISearchableBar

Creates PathManagerUI's SearchableBar

PathMatcherCmd - Class in sc.fiji.snt.plugin

Command for matching Paths across time-points (time-lapse analysis).

PathMatcherCmd() - Constructor for class sc.fiji.snt.plugin.PathMatcherCmd

PathNode(double, double, double) - Constructor for class sc.fiji.snt.Path.PathNode

PathNode(SNTPoint) - Constructor for class sc.fiji.snt.Path.PathNode

PathNodeCanvas - Class in sc.fiji.snt

Convenience class used to render Path nodes (vertices) in an TracerCanvas.

PathNodeCanvas(Path, int, TracerCanvas) - Constructor for class sc.fiji.snt.PathNodeCanvas

Creates a node from a Path position.

PathNodeCanvas(PointInImage, int, TracerCanvas) - Constructor for class sc.fiji.snt.PathNodeCanvas

Creates a path node from a PointInImage.

PathOrderAnalysisCmd - Class in sc.fiji.snt.plugin

Command to perform Path Ordering analysis on a Tree.

PathOrderAnalysisCmd(Tree) - Constructor for class sc.fiji.snt.plugin.PathOrderAnalysisCmd

PathOverlap() - Constructor for class sc.fiji.snt.analysis.curation.PlausibilityCheck.PathOverlap

PathProfiler - Class in sc.fiji.snt.analysis

Command to retrieve Path profiles (plots of voxel intensities values along a Path)

PathProfiler() - Constructor for class sc.fiji.snt.analysis.PathProfiler

Empty constructor used by CommandService before calling PathProfiler.run().

PathProfiler(Path, ImagePlus) - Constructor for class sc.fiji.snt.analysis.PathProfiler

Deprecated.

Use PathProfiler(Path, Dataset)

PathProfiler(Path, Dataset) - Constructor for class sc.fiji.snt.analysis.PathProfiler

Instantiates a new Profiler from a single path.

PathProfiler(Tree, ImagePlus) - Constructor for class sc.fiji.snt.analysis.PathProfiler

Deprecated.

Use PathProfiler(Tree, Dataset)

PathProfiler(Tree, Dataset) - Constructor for class sc.fiji.snt.analysis.PathProfiler

Instantiates a new Profiler.

PathRenderingOptions() - Constructor for class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

paths - Variable in class sc.fiji.snt.analysis.TreeColorMapper

PathSpineAnalysisCmd - Class in sc.fiji.snt.plugin

Command for obtaining plots pertaining to spine/varicosity counts

PathSpineAnalysisCmd() - Constructor for class sc.fiji.snt.plugin.PathSpineAnalysisCmd

PathStatistics - Class in sc.fiji.snt.analysis

A specialized version of TreeStatistics for analyzing individual paths without considering their connectivity relationships.

PathStatistics(Collection<Path>, String) - Constructor for class sc.fiji.snt.analysis.PathStatistics

Instantiates PathStatistics from a collection of paths.

PathStatistics(Path) - Constructor for class sc.fiji.snt.analysis.PathStatistics

Instantiates PathStatistics from a single path.

pathsToIDListString(ArrayList<Path>) - Static method in class sc.fiji.snt.Path

PathStraightener - Class in sc.fiji.snt.analysis

Command to "straighten" an image using Path coordinates.

PathStraightener(Path, ImagePlus) - Constructor for class sc.fiji.snt.analysis.PathStraightener

Instantiates a new PathStraightener

PathStraightener(Path, SNT) - Constructor for class sc.fiji.snt.analysis.PathStraightener

Instantiates a new PathStraightener

PathTimeAnalysisCmd - Class in sc.fiji.snt.plugin

Command for obtaining 'time-profiles' of Paths (time-lapse analysis).

PathTimeAnalysisCmd() - Constructor for class sc.fiji.snt.plugin.PathTimeAnalysisCmd

PathTransformer - Interface in sc.fiji.snt

Classes transforming Paths should implement this interface.

pause(boolean) - Method in class sc.fiji.snt.SNTUI

Pauses/Resume SNT (equivalent to command in image contextual menu).

pause(boolean, boolean) - Method in class sc.fiji.snt.SNT

pauseTracing(boolean) - Method in class sc.fiji.snt.SNTUI

Pauses/Resume tracing functions (equivalent to command in image contextual menu).

pauseTracing(boolean, boolean) - Method in class sc.fiji.snt.SNT

PCAnalyzer - Class in sc.fiji.snt.analysis

Utility class for performing Principal Component Analysis (PCA) on various SNT data structures including Trees, Paths, and collections of SNTPoints.

PCAnalyzer() - Constructor for class sc.fiji.snt.analysis.PCAnalyzer

PCAnalyzer.PrincipalAxis - Class in sc.fiji.snt.analysis

Represents a principal axis containing the direction vector and associated variance (eigenvalue) from Principal Component Analysis.

pd() - Method in record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.Report

Returns the value of the pd record component.

PEN - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

percentage() - Method in class sc.fiji.snt.gui.GuiUtils.JTables.VisitingZoom

percentileUsed() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCalibrator.CheckSummary

Returns the value of the percentileUsed record component.

PERIMETER - Static variable in interface sc.fiji.snt.analysis.sholl.math.ShollStats

Flag for perimeter normalization (Semi-log/Log-log method)

PeripathDetector - Class in sc.fiji.snt.analysis.detection

Detects intensity maxima (varicosities, spines, synaptic puncta) in annular cross-sections around traced paths.

PeripathDetector - Class in sc.fiji.snt.analysis

Deprecated.

Use PeripathDetector instead. This class is retained for backward compatibility and delegates all calls to the new package.

PeripathDetector.Config - Class in sc.fiji.snt.analysis.detection

Immutable configuration with builder-like setters.

PeripathDetector.Config - Class in sc.fiji.snt.analysis

Deprecated.

Use PeripathDetector.Config instead.

PeripathDetector.Detection - Class in sc.fiji.snt.analysis

Deprecated.

Use Detection instead.

PeripathDetectorCmd - Class in sc.fiji.snt.gui.cmds

SciJava command for detecting varicosities/spines/puncta flanking traced paths.

PeripathDetectorCmd() - Constructor for class sc.fiji.snt.gui.cmds.PeripathDetectorCmd

PERIPHERAL_SEGMENTS - Static variable in class sc.fiji.snt.tracing.auto.BinaryTracer

Pruning mode: flag for lowest centrality edge pruning (preserves backbone).

permuteToXYZCT(ImgPlus<T>) - Static method in class sc.fiji.snt.util.ImgUtils

Reorders the axes of an ImgPlus to the canonical XYZCT order expected by BVV and most ImageJ tools, applying swaps as needed.

persistenceAnalysis() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

PersistenceAnalyzer - Class in sc.fiji.snt.analysis

Performs persistent homology analysis on neuronal Trees.

PersistenceAnalyzer(Tree) - Constructor for class sc.fiji.snt.analysis.PersistenceAnalyzer

Creates a new PersistenceAnalyzer for the specified neuronal tree.

PersistenceAnalyzerCmd - Class in sc.fiji.snt.gui.cmds

GUI command persistent homology analyses.

PersistenceAnalyzerCmd() - Constructor for class sc.fiji.snt.gui.cmds.PersistenceAnalyzerCmd

PERSON_CHALKBOARD - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

PERSPECTIVE - Enum constant in enum class sc.fiji.snt.viewer.Viewer3D.ViewMode

Enforce an 'overview' (two-point perspective) view point of the scene.

physicalSizes() - Method in record class sc.fiji.snt.io.OmeAxisUtils.OmeMetadata

Returns the value of the physicalSizes record component.

physicalUnits() - Method in record class sc.fiji.snt.io.OmeAxisUtils.OmeMetadata

Returns the value of the physicalUnits record component.

PING_PONG - Enum constant in enum class sc.fiji.snt.viewer.Viewer3D.AnimationMode

Oscillating rotation that rocks back and forth over a fixed arc.

plane - Variable in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

PLANE - Static variable in class sc.fiji.snt.viewer.Annotation3D

PLASMA - Static variable in class sc.fiji.snt.util.ColorMaps

PLATEAU - Enum constant in enum class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhaseType

Plateau phase - minimal growth

PlausibilityCalibrator - Class in sc.fiji.snt.analysis.curation

Infers PlausibilityCheck thresholds from a collection of reference Trees.

PlausibilityCalibrator(Collection<Tree>) - Constructor for class sc.fiji.snt.analysis.curation.PlausibilityCalibrator

Creates a calibrator from a collection of reference trees.

PlausibilityCalibrator.CalibrationResult - Class in sc.fiji.snt.analysis.curation

Aggregated calibration results from a set of reference trees.

PlausibilityCalibrator.CheckSummary - Record Class in sc.fiji.snt.analysis.curation

Summary for a single calibrated parameter.

PlausibilityCheck - Class in sc.fiji.snt.analysis.curation

Framework for evaluating the morphological plausibility of path operations and reconstructions.

PlausibilityCheck.BranchAngle - Class in sc.fiji.snt.analysis.curation

Warns when the bifurcation angle at a fork is outside a plausible range.

PlausibilityCheck.ConstantRadii - Class in sc.fiji.snt.analysis.curation

Warns when a path has radii assigned but they are all identical (likely unfitted defaults).

PlausibilityCheck.DeepCheck - Class in sc.fiji.snt.analysis.curation

A heavier check that scans an entire collection of paths for issues.

PlausibilityCheck.DirectionContinuity - Class in sc.fiji.snt.analysis.curation

Warns when the child path's initial direction deviates sharply from the parent's tangent at the branch point (potential U-turn).

PlausibilityCheck.LiveCheck - Class in sc.fiji.snt.analysis.curation

A lightweight check that evaluates the plausibility of a single fork operation (parent + child + branch index).

PlausibilityCheck.PathOverlap - Class in sc.fiji.snt.analysis.curation

Detects paths that run very close to each other without being topologically connected.

PlausibilityCheck.RadiusContinuity - Class in sc.fiji.snt.analysis.curation

Warns when the child neurite's radius at the fork point exceeds the parent's radius at the branch point.

PlausibilityCheck.RadiusJumps - Class in sc.fiji.snt.analysis.curation

Detects abrupt radius jumps between adjacent nodes within a path.

PlausibilityCheck.RadiusMonotonicity - Class in sc.fiji.snt.analysis.curation

Detects sustained radius increases along a path (neurites should generally taper distally).

PlausibilityCheck.Severity - Enum Class in sc.fiji.snt.analysis.curation

Severity levels for plausibility warnings.

PlausibilityCheck.SignalQuality - Class in sc.fiji.snt.analysis.curation

Assesses local image signal quality around traced paths and flags those in regions with poor contrast.

PlausibilityCheck.SomaDistance - Class in sc.fiji.snt.analysis.curation

Warns when a primary path starts far from any soma node.

PlausibilityCheck.TerminalBranchLength - Class in sc.fiji.snt.analysis.curation

Warns when a terminal branch is suspiciously short.

PlausibilityCheck.TortuosityConsistency - Class in sc.fiji.snt.analysis.curation

Warns when child and parent have very different tortuosity (contraction).

PlausibilityCheck.Warning - Record Class in sc.fiji.snt.analysis.curation

A plausibility warning produced by a check.

PlausibilityMonitor - Class in sc.fiji.snt.analysis.curation

Monitors tracing and editing operations for morphological plausibility.

PlausibilityMonitor() - Constructor for class sc.fiji.snt.analysis.curation.PlausibilityMonitor

PlausibilityMonitor.WarningListener - Interface in sc.fiji.snt.analysis.curation

Listener interface for warning list changes.

playback(List<Bvv.Keyframe>) - Method in class sc.fiji.snt.viewer.Bvv

Plays back an animation between keyframes in the viewer without saving frames.

playback(List<Bvv.Keyframe>, int, int) - Method in class sc.fiji.snt.viewer.Bvv

Plays back a subset of keyframes (from index from to index to, inclusive).

plot - Variable in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

plot - Variable in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

plot - Variable in class sc.fiji.snt.viewer.Viewer2D

plot() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

plot() - Method in class sc.fiji.snt.analysis.sholl.Profile

PlotterCmd - Class in sc.fiji.snt.plugin

Implements Reconstruction Plotter, a command wrapper for interactively plotting trees using Viewer2D

PlotterCmd() - Constructor for class sc.fiji.snt.plugin.PlotterCmd

plugin - Variable in class sc.fiji.snt.PathAndFillManager

PLUS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

po() - Method in record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.Report

Returns the value of the po record component.

PointDeduplicator - Class in sc.fiji.snt.util

Greedy non-maximum suppression (NMS) for scored 3D points.

PointDeduplicator(List<? extends SNTPoint>, double[], double) - Constructor for class sc.fiji.snt.util.PointDeduplicator

Creates a new deduplicator.

POINTER - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

PointInCanvas - Class in sc.fiji.snt.util

Defines a Point in a tracing canvas in pixel coordinates.

PointInCanvas(double, double, double) - Constructor for class sc.fiji.snt.util.PointInCanvas

Constructs a new PointInCanvas with the specified coordinates.

PointInCanvas(double, double, double, Path) - Constructor for class sc.fiji.snt.util.PointInCanvas

PointInImage - Class in sc.fiji.snt.util

Defines a Point in an image, a node of a traced Path.

PointInImage() - Constructor for class sc.fiji.snt.util.PointInImage

PointInImage(double, double, double) - Constructor for class sc.fiji.snt.util.PointInImage

PointInImage(double, double, double, Path) - Constructor for class sc.fiji.snt.util.PointInImage

points - Variable in class sc.fiji.snt.analysis.AbstractConvexHull

points - Variable in class sc.fiji.snt.analysis.sholl.ProfileEntry

List of intersection points associated with the entry's radius (in spatially calibrated units)

points() - Method in class sc.fiji.snt.analysis.sholl.Profile

POINTS - Static variable in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

POINTS_EXHAUSTED - Static variable in class sc.fiji.snt.tracing.SearchThread

pointsConsideredInSearch() - Method in class sc.fiji.snt.tracing.AbstractSearch

Returns the total number of points evaluated so far during the search.

pointsConsideredInSearch() - Method in class sc.fiji.snt.tracing.BiSearch

pointsConsideredInSearch() - Method in class sc.fiji.snt.tracing.SearchThread

pointsInSearch(SearchInterface, long, long) - Method in class sc.fiji.snt.FillManagerUI

pointsInSearch(SearchInterface, long, long) - Method in interface sc.fiji.snt.SearchProgressCallback

pointsInSearch(SearchInterface, long, long) - Method in class sc.fiji.snt.SNT

PolarPeak(double, double, int) - Constructor for record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.PolarPeak

Creates an instance of a PolarPeak record class.

polarPlot(String, List<double[][]>, List<Color>) - Static method in class sc.fiji.snt.analysis.AnalysisUtils

Generates a polar plot

PolarProfileStats - Class in sc.fiji.snt.analysis.sholl.math

PolarProfileStats computes angle-resolved (‘Polar Sholl’) metrics from a Sholl Profile, providing analysis and visualization methods for directional patterns in Sholl profiles.

PolarProfileStats(LinearProfileStats, double) - Constructor for class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Instantiates a new PolarProfileStats from a Profile with custom angular resolution.

PolarProfileStats(Profile) - Constructor for class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Instantiates a new PolarProfileStats from an existing Sholl Profile, with the default angular resolution (10°).

PolarProfileStats(Profile, ShollStats.DataMode, double) - Constructor for class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Instantiates a new PolarProfileStats from a Profile with custom angular resolution.

PolarProfileStats.PolarPeak - Record Class in sc.fiji.snt.analysis.sholl.math

Simple container for angular peaks.

PolarProfileStats.Report - Record Class in sc.fiji.snt.analysis.sholl.math

Immutable summary of the global polar distribution.

POLY_FIT_DEGREE - Static variable in class sc.fiji.snt.analysis.ShollAnalyzer

populateImpChoices(Predicate<ImagePlus>) - Method in class sc.fiji.snt.gui.cmds.ChooseDatasetCmd

Populates ChooseDatasetCmd.impMap and the "choice" parameter's widget with the titles of all open ImagePlus instances, excluding the SNT main tracing image (when present) and any image rejected by the optional filter.

popupMenu - Variable in class sc.fiji.snt.gui.GuiUtils.Buttons.OptionsButton

positive() - Method in record class sc.fiji.snt.analysis.curation.CurationTags.Partition

Returns the value of the positive record component.

POSITIVE - Static variable in class sc.fiji.snt.analysis.curation.CurationTags

Tag value applied to paths accepted during review.

posToIndex(long[]) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

posToIndex(long[], long[]) - Static method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Converts an N-dimensional position to a flat array index using row-major order.

precomputeNeighborDistances() - Method in class sc.fiji.snt.tracing.AbstractSearch

Precompute distances to all 27 neighbors (including self at 0,0,0).

precomputeNeighborDistances() - Method in class sc.fiji.snt.tracing.FillerThread

Precompute distances to all 27 neighbors (including self at 0,0,0).

predecessor - Variable in class sc.fiji.snt.tracing.DefaultSearchNode

PrefsCmd - Class in sc.fiji.snt.gui.cmds

Command for (re)setting SNT Preferences.

PrefsCmd() - Constructor for class sc.fiji.snt.gui.cmds.PrefsCmd

prepareRadii(Path) - Static method in class sc.fiji.snt.analysis.detection.DetectorUtils

Prepares a sanitized radius array for the given path.

preview() - Method in class sc.fiji.snt.gui.cmds.TranslateReconstructionsCmd

preview() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCommonCmd

preview() - Method in class sc.fiji.snt.plugin.ShollAnalysisTreeCmd

previous - Variable in class sc.fiji.snt.Fill.Node

previous() - Method in class sc.fiji.snt.util.SWCPoint

Returns the preceding node (if any)

PREVIOUS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

previousZoomLevel(double) - Static method in class sc.fiji.snt.util.ImpUtils

PRIMARY_EXTENSION_ANGLE - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Primary branches: Extension angle"

PRIMARY_EXTENSION_ANGLE_XY - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Primary branches: Extension angle XY"

PRIMARY_EXTENSION_ANGLE_XZ - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Primary branches: Extension angle XZ"

PRIMARY_EXTENSION_ANGLE_ZY - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Primary branches: Extension angle ZY"

PRIMARY_LENGTH - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics

Flag for "Length of primary branches (sum)" analysis.

PRIMARY_LENGTH - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Primary branches: Length"

primaryBranches - Variable in class sc.fiji.snt.analysis.TreeStatistics

print(String) - Method in class sc.fiji.snt.gui.SNTInterpreterPane

Prints a message to the output panel.

print(String) - Method in class sc.fiji.snt.gui.SNTInterpreterWindow

Prints a message to the output panel.

printMemoryStatus() - Static method in class sc.fiji.snt.tracing.auto.GWDTTracerFactory

Print current memory status and thresholds to console.

printStatus() - Method in class sc.fiji.snt.tracing.AbstractSearch

Prints the current search status to the log.

printStatus() - Method in class sc.fiji.snt.tracing.BiSearch

printStatus() - Method in class sc.fiji.snt.tracing.SearchThread

PROBABILITY - Enum constant in enum class sc.fiji.snt.SNT.CostType

process() - Method in class sc.fiji.snt.analysis.ProfileProcessor

Processes the profile data by calling the computation.

process(Interval, int[], T, Consumer<RandomAccessibleInterval<T>>) - Static method in class sc.fiji.snt.filter.Lazy

Create a DiskCachedCellImg with a cell generator Consumer.

process(RandomAccessibleInterval<I>, Interval, int[], O, OpService, Class<P>, Object...) - Static method in class sc.fiji.snt.filter.Lazy

Create a DiskCachedCellImg with a cell generator UnaryComputerOp provided by an OpService.

process(RandomAccessibleInterval<I>, Interval, int[], O, UnaryComputerOp<RandomAccessibleInterval<I>, RandomAccessibleInterval<O>>) - Static method in class sc.fiji.snt.filter.Lazy

Create a DiskCachedCellImg with a cell generator UnaryComputerOp.

profile - Variable in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

profile - Variable in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

profile - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

Profile - Class in sc.fiji.snt.analysis.sholl

Defines a Sholl profile

Profile() - Constructor for class sc.fiji.snt.analysis.sholl.Profile

Instantiates a new empty profile.

Profile(double[][]) - Constructor for class sc.fiji.snt.analysis.sholl.Profile

Constructor accepting matrices.

Profile(Number[], Number[]) - Constructor for class sc.fiji.snt.analysis.sholl.Profile

Legacy constructor accepting arrays.

Profile(List<Number>, List<Number>) - Constructor for class sc.fiji.snt.analysis.sholl.Profile

Default constructor.

ProfileEntry - Class in sc.fiji.snt.analysis.sholl

Utility class defining a Sholl profile entry

ProfileEntry(Number, Number) - Constructor for class sc.fiji.snt.analysis.sholl.ProfileEntry

ProfileEntry(Number, Number, Number) - Constructor for class sc.fiji.snt.analysis.sholl.ProfileEntry

ProfileEntry(Number, Number, Number, Set<ShollPoint>) - Constructor for class sc.fiji.snt.analysis.sholl.ProfileEntry

ProfileEntry(Number, Number, Set<ShollPoint>) - Constructor for class sc.fiji.snt.analysis.sholl.ProfileEntry

ProfileEntry(Number, Set<ShollPoint>) - Constructor for class sc.fiji.snt.analysis.sholl.ProfileEntry

profilePathNodes(RandomAccessible<T>, Path, double[]) - Static method in class sc.fiji.snt.analysis.ProfileProcessor

Get the intensities for the point coordinates of a Path

ProfileProcessor<T> - Class in sc.fiji.snt.analysis

Profile intensities within local neighborhoods around Path PointInImages

ProfileProcessor(RandomAccessibleInterval<T>, Path) - Constructor for class sc.fiji.snt.analysis.ProfileProcessor

ProfileProcessor.Metric - Enum Class in sc.fiji.snt.analysis

ProfileProcessor.Shape - Enum Class in sc.fiji.snt.analysis

ProfileProperties - Interface in sc.fiji.snt.analysis.sholl

Associates metadata to a Sholl Profile

progressListeners - Variable in class sc.fiji.snt.tracing.AbstractSearch

progressListeners - Variable in class sc.fiji.snt.tracing.TubularGeodesicsTracer

prominence(double) - Method in class sc.fiji.snt.analysis.detection.PeripathDetector.Config

promptForAutoTracingAsAppropriate() - Method in class sc.fiji.snt.SNTUI

PROP - Static variable in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

properties - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

proportionDone(double) - Method in interface sc.fiji.snt.HessianGenerationCallback

proportionDone(double) - Method in class sc.fiji.snt.SNT

proximity(double) - Method in class sc.fiji.snt.util.CrossoverFinder.Config

Sets CrossoverFinder.Config.proximity.

pruneByLength - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

pruneModeToString(BinaryTracer) - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

Returns a human-readable string for the current prune mode of the given tracer.

pruneParallelBranches(DirectedWeightedGraph) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Prunes parallel sibling branches, i.e., pairs of terminal branches that fork from the same branch point and then run alongside each other (their nodes stay within a radius-dependent proximity threshold).

Q

Q_TIP - Static variable in class sc.fiji.snt.viewer.Annotation3D

QUESTION - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

quickMeasurementsCmdError(GuiUtils) - Method in class sc.fiji.snt.PathManagerUI

quit() - Method in class sc.fiji.snt.gui.SNTPromptPane

A callback method which is invoked when the REPL quits.

QUIT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

QUIT - Static variable in class sc.fiji.snt.event.SNTEvent

Event type indicating a quit/exit event

R

ra - Variable in class sc.fiji.snt.util.CircleCursor3D

radii - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

radii() - Method in class sc.fiji.snt.analysis.sholl.Profile

RADII - Static variable in class sc.fiji.snt.PathFitter

Flag specifying that the computed path should only inherit fitted radii attributes

RADII_AND_MIDPOINTS - Static variable in class sc.fiji.snt.PathFitter

Flag specifying that the computed path should inherit both midpoint refinement of node coordinates and radii

radiiAsArray() - Method in class sc.fiji.snt.analysis.sholl.Profile

radiiSquared() - Method in class sc.fiji.snt.analysis.sholl.Profile

radius - Variable in class sc.fiji.snt.analysis.sholl.ProfileEntry

The entry's radius length (in physical units)

radius - Variable in class sc.fiji.snt.seed.SeedPoint

Estimated radius in physical units.

radius - Variable in class sc.fiji.snt.util.CircleCursor3D

radius - Variable in class sc.fiji.snt.util.PointInImage

The radius of reconstructed structure at this node

radius() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Returns the value of the radius record component.

RADIUS - Enum constant in enum class sc.fiji.snt.tracing.auto.AbstractGWDTTracer.WaypointBiasSource

Bias proportional to each seed's radius (normalised over the waypoint set).

RADIUS - Static variable in class sc.fiji.snt.analysis.NodeColorMapper

Flag for "Node radius" statistics.

RADIUS - Static variable in class sc.fiji.snt.analysis.NodeStatistics

Flag for "Node radius" statistics.

RADIUS - Static variable in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

RADIUS_WEIGHT_KEY - Static variable in class sc.fiji.snt.gui.cmds.MultiSpectralRefinerCmd

RadiusContinuity() - Constructor for class sc.fiji.snt.analysis.curation.PlausibilityCheck.RadiusContinuity

RadiusJumps() - Constructor for class sc.fiji.snt.analysis.curation.PlausibilityCheck.RadiusJumps

RadiusMonotonicity() - Constructor for class sc.fiji.snt.analysis.curation.PlausibilityCheck.RadiusMonotonicity

radiusScaleFactor - Variable in class sc.fiji.snt.gui.cmds.mxOrganicLayoutPrefsCmd

The factor by which the moveRadius is multiplied by after every iteration.

radiusSquared() - Method in class sc.fiji.snt.analysis.sholl.ProfileEntry

radiusWeight() - Method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Returns the value of the radiusWeight record component.

rai - Variable in class sc.fiji.snt.util.CircleCursor3D

raiToImp(RandomAccessibleInterval<T>, String) - Static method in class sc.fiji.snt.util.ImgUtils

Convert a RandomAccessibleInterval to an ImagePlus.

RAMIFICATION_INDEX - Static variable in class sc.fiji.snt.analysis.ShollAnalyzer

randomPaths() - Static method in class sc.fiji.snt.SNTUtils

Generates a list of random paths.

RAPID - Enum constant in enum class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhaseType

Rapid phase - fast growth

rasterize() - Method in class sc.fiji.snt.util.TreeToRaster

Rasterizes the tree into a 32-bit (float) image using partial-volume supersampling.

rasterize(Tree) - Static method in class sc.fiji.snt.util.TreeUtils

Rasterizes a tree into a 3D image using frustum (truncated-cone) geometry with partial-volume supersampling.

rasterize(Tree, double, double) - Static method in class sc.fiji.snt.util.TreeUtils

Rasterizes a tree into a 3D image with the specified voxel sizes.

rasterizeLabels() - Method in class sc.fiji.snt.util.TreeToRaster

Deprecated.

Use TreeToRaster.rasterizePathLabels() instead

rasterizeNodeValueLabels() - Method in class sc.fiji.snt.util.TreeToRaster

Rasterizes the tree into a 16-bit label image where each voxel is assigned the node value of the nearest path node (as stored via Path.setNodeValue(double, int)).

rasterizePathLabels() - Method in class sc.fiji.snt.util.TreeToRaster

Rasterizes the tree into a 16-bit label image where each voxel is assigned the 1-based index of the Path that owns it (as ordered by Tree.list()).

rate() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.ElongationEvent

Returns the value of the rate record component.

rate() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.RetractionEvent

Returns the value of the rate record component.

rawX(Calibration) - Method in class sc.fiji.snt.util.ShollPoint

rawY(Calibration) - Method in class sc.fiji.snt.util.ShollPoint

rawZ(Calibration) - Method in class sc.fiji.snt.util.ShollPoint

rBar() - Method in record class sc.fiji.snt.analysis.CircularModels.VonMisesFit

Returns the value of the rBar record component.

readParameters() - Static method in class sc.fiji.snt.gui.cmds.MultiSpectralRefinerCmd

Reads stored preferences and returns a MultiSpectralRefiner.Parameters record, or defaults if no preferences have been stored.

readPreferences() - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Reads stored preferences from MultiSpectralRefinerCmd and applies them to this refiner.

readPreferences() - Method in class sc.fiji.snt.PathFitter

READY - Enum constant in enum class sc.fiji.snt.FillManagerUI.State

READY - Static variable in class sc.fiji.snt.SNTUI

Flag specifying that image data is available and the UI is not waiting on any pending operations, thus 'ready to trace'

rebuild() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

rebuild(Object) - Method in class sc.fiji.snt.viewer.Viewer3D

Rebuilds (repaints) a scene object (e.g., a Tree after being modified elsewhere)

rebuild(ShollStats) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

rebuildConnectionsOfFittedVersion() - Method in class sc.fiji.snt.Path

rebuildDisplayCanvases() - Method in class sc.fiji.snt.SNT

Rebuilds display canvases, i.e., the placeholder canvases used when no valid image data exists (a single-canvas is rebuilt if only the XY view is active).

rebuildGraph() - Method in class sc.fiji.snt.Tree

Re-assembles the DirectedGraph object returned by Tree.getGraph() ensuring that no untracked changes exist.

rebuildRelationships() - Method in class sc.fiji.snt.PathAndFillManager

Rebuild relationships.

rebuildZYXZpanes() - Method in class sc.fiji.snt.SNT

recalculateRadiiFromImage(DirectedWeightedGraph, double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Recalculates radii for all nodes using image-based method (like APP2).

Reciprocal - Class in sc.fiji.snt.tracing.cost

Uses the reciprocal of voxel intensity, rescaled to the interval (double precision) 255 * (intensity - min) / (max - min) to compute the cost of moving to a neighbor node.

Reciprocal(double, double) - Constructor for class sc.fiji.snt.tracing.cost.Reciprocal

RECIPROCAL - Enum constant in enum class sc.fiji.snt.SNT.CostType

RECIPROCAL_FUDGE - Static variable in class sc.fiji.snt.tracing.cost.Reciprocal

recolorTracks(JScrollPane, Color, boolean) - Static method in class sc.fiji.snt.gui.GuiUtils

recommendBackend(long[]) - Static method in class sc.fiji.snt.tracing.auto.GWDTTracerFactory

Get recommended storage backend type for an image.

recomputeStatuses() - Method in class sc.fiji.snt.seed.SeedTableModel

Recomputes the coverage cache and fires a status-column update.

reconnect(DirectedWeightedGraph, SWCPoint, double) - Method in class sc.fiji.snt.tracing.auto.ComponentReconnector

Attempts to reconnect disconnected components in the graph back to the main tree (the component containing the root).

ReconstructionViewerCmd - Class in sc.fiji.snt.gui.cmds

Command for starting Reconstruction Viewer as a 'stand-alone' program

ReconstructionViewerCmd() - Constructor for class sc.fiji.snt.gui.cmds.ReconstructionViewerCmd

reconstructPath(double, double, double, String) - Method in class sc.fiji.snt.tracing.BiSearch

recordCmd(String) - Method in class sc.fiji.snt.gui.ScriptRecorder

recordCmd(String, boolean) - Method in class sc.fiji.snt.gui.ScriptRecorder

recordComment(String) - Method in class sc.fiji.snt.gui.ScriptRecorder

recordRotation(float, int, File) - Method in class sc.fiji.snt.viewer.Viewer3D

Records an animated rotation of the scene as a sequence of images.

recordRotation(float, int, File, Viewer3D.RotationAxis) - Method in class sc.fiji.snt.viewer.Viewer3D

Records an animated rotation of the scene around the specified axis as a sequence of images.

recViewer - Variable in class sc.fiji.snt.SNTUI

recViewerFrame - Variable in class sc.fiji.snt.SNTUI

RecViewerPrefsCmd - Class in sc.fiji.snt.gui.cmds

Command implementing Reconstruction Viewer 'Preferences...' command.

RecViewerPrefsCmd() - Constructor for class sc.fiji.snt.gui.cmds.RecViewerPrefsCmd

RECYCLE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

REDO - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

REF_WINDOW_KEY - Static variable in class sc.fiji.snt.gui.cmds.MultiSpectralRefinerCmd

referenceWindowRadius() - Method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Returns the value of the referenceWindowRadius record component.

refineTree(ImagePlus, Tree) - Static method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Refines all paths in a tree, processing each path in parallel.

refineTree(ImagePlus, Tree, MultiSpectralRefiner.Parameters) - Static method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Refines all paths in a tree with custom parameters.

refineTree(ImgPlus<T>, Tree) - Static method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Refines all paths in a tree, processing each path in parallel.

refineTree(ImgPlus<T>, Tree, MultiSpectralRefiner.Parameters) - Static method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Refines all paths in a tree with custom parameters.

reflectionMatrix(double[], double[]) - Static method in class sc.fiji.snt.util.LinAlgUtils

4x4 Householder reflection matrix

refresh() - Method in class sc.fiji.snt.SNTUI

Updates the dialog, including status bar and 'computation settings' widget.

refresh() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

refresh() - Method in class sc.fiji.snt.viewer.geditor.SNTGraphComponent

refreshForPaths(Collection<Path>) - Method in class sc.fiji.snt.PathManagerUI

Repaints the Path Manager view for the given paths.

refreshFromMonitor() - Method in class sc.fiji.snt.CurationManager

Refreshes all UI controls (spinners, checkboxes, toggle) from the monitor's current state.

REGEX_BUTTON - Static variable in class sc.fiji.snt.gui.SearchField

regexButton() - Method in class sc.fiji.snt.gui.SearchField

register(AbstractButton, String...) - Method in class sc.fiji.snt.gui.SNTCommandFinder

register(AbstractButton, List<String>) - Method in class sc.fiji.snt.gui.SNTCommandFinder

register(JPopupMenu, List<String>) - Method in class sc.fiji.snt.gui.SNTCommandFinder

registerCommands(SNTCommandFinder) - Method in class sc.fiji.snt.CurationManager

Registers curation commands in the SNT Command Finder.

registerComponent(Component...) - Method in class sc.fiji.snt.gui.ComponentMover

Add the required listeners to the specified component

reinitializeFastMarching(long[], long, Set<Long>) - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

reinitializeFastMarching(long[], long, Set<Long>) - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

reinitializeFastMarching(long[], long, Set<Long>) - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

reinitializeFastMarching(long[], long, Set<Long>) - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Re-initializes Fast Marching data structures (distances, parents, state) while preserving the pre-computed GWDT.

reload() - Method in class sc.fiji.snt.PathManagerUI

Reloads the contents of PathAndFillManager

reloadFills(int[]) - Method in class sc.fiji.snt.PathAndFillManager

reloadImage(int, int) - Method in class sc.fiji.snt.SNT

reloadZYXZpanes(int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

REMOTE_BIF_ANGLES - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Remote bifurcation angles"

RemoteSWCImporterCmd - Class in sc.fiji.snt.gui.cmds

Command for importing SWC reconstructions from remote databases

RemoteSWCImporterCmd() - Constructor for class sc.fiji.snt.gui.cmds.RemoteSWCImporterCmd

RemoteSWCLoader - Interface in sc.fiji.snt.io

Importers downloading remote SWC files should extend this interface.

remove() - Method in class sc.fiji.snt.PathAndFillManager.AllPointsIterator

remove(Overlay, String) - Static method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

remove(Component) - Static method in class sc.fiji.snt.gui.FileDrop

Removes the drag-and-drop hooks from the component and optionally from the all children.

remove(PrintStream, Component, boolean) - Static method in class sc.fiji.snt.gui.FileDrop

Removes the drag-and-drop hooks from the component and optionally from the all children.

remove(Object) - Method in class sc.fiji.snt.viewer.Viewer3D

Script friendly method to remove an object (Tree, OBJMesh, AbstractDrawable, String (object label), etc.) from this viewer's scene.

remove(Path) - Method in class sc.fiji.snt.Tree

Removes a path from this tree.

remove(Path, int) - Method in class sc.fiji.snt.BookmarkManager

remove(SeedPoint) - Method in class sc.fiji.snt.seed.SeedOverlay

Removes a single seed by reference equality.

removeAll(Collection<? extends SeedPoint>) - Method in class sc.fiji.snt.seed.SeedOverlay

Bulk-removes seeds by reference equality.

removeAllAnnotations() - Method in class sc.fiji.snt.viewer.Viewer3D

Removes all the Annotations from current viewer

removeAllMeshes() - Method in class sc.fiji.snt.viewer.Viewer3D

Removes all loaded OBJ meshes from current viewer

removeAllTrees() - Method in class sc.fiji.snt.viewer.Viewer3D

Removes all the Trees from current viewer

removeAnnotation(String) - Method in class sc.fiji.snt.viewer.Viewer3D

Removes the annotation with the specified label from the viewer.

removeAnnotation(Annotation3D) - Method in class sc.fiji.snt.viewer.Viewer3D

Removes the specified annotation from the viewer.

removeAt(int) - Method in class sc.fiji.snt.seed.SeedOverlay

Removes the seed at the given (data-list) index.

removeChangeListener(PathChangeListener) - Method in class sc.fiji.snt.Path

removeColumn(String) - Method in class sc.fiji.snt.analysis.SNTTable

removeDisconnectedComponents(DirectedWeightedGraph) - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Removes all vertices not connected to the root.

removeFrom3DViewer(Image3DUniverse) - Method in class sc.fiji.snt.Path

Deprecated.

This method is deprecated. Use newer 3D visualization methods instead.

removeFromBvv() - Method in class sc.fiji.snt.viewer.BvvMultiSource

Removes all sources in the group from the viewer.

removeIcon(Object) - Static method in class sc.fiji.snt.gui.GuiUtils

removeIsolatedPixels(ImagePlus) - Static method in class sc.fiji.snt.util.ImpUtils

removeListener(SigmaPaletteListener) - Method in class sc.fiji.snt.gui.SigmaPalette

removeListener(SeedOverlay.SeedOverlayListener) - Method in class sc.fiji.snt.seed.SeedOverlay

Removes a listener (no-op if not registered).

removeMesh(String) - Method in class sc.fiji.snt.viewer.Viewer3D

Removes the specified OBJ mesh.

removeMesh(OBJMesh) - Method in class sc.fiji.snt.viewer.Viewer3D

Removes the specified OBJ mesh.

removeMIPOverlayAllPanes() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

removeMIPOverlayAllPanes(String...) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

removeNode(int) - Method in class sc.fiji.snt.Path

Removes the specified node if this path has at least two nodes.

removeOrphans() - Method in class sc.fiji.snt.analysis.graph.AnnotationGraph

removeOvershoots(DirectedWeightedGraph) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Removes overshoot artifacts from the graph.

removePoint(ShollPoint) - Method in class sc.fiji.snt.analysis.sholl.ProfileEntry

removePoints() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

removeSearchArtist(SearchArtist) - Method in class sc.fiji.snt.TracerCanvas

removeSelected() - Method in class sc.fiji.snt.seed.SeedOverlay

Removes all currently selected seeds from the data list.

removeShells() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

removeShells(Overlay) - Static method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

removeShollROIs(Overlay) - Static method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

removeSlices(ImageStack, Collection<String>) - Static method in class sc.fiji.snt.util.ImpUtils

removeSphere(String) - Method in class sc.fiji.snt.SNT

removeSummary() - Method in class sc.fiji.snt.analysis.SNTTable

Removes summary statistics from the table.

removeTree(String) - Method in class sc.fiji.snt.viewer.Bvv

removeTree(String) - Method in class sc.fiji.snt.viewer.Viewer3D

Removes the specified Tree.

removeTree(Tree) - Method in class sc.fiji.snt.SciViewSNT

Removes the specified Tree.

removeTree(Tree) - Method in class sc.fiji.snt.viewer.Viewer3D

Removes the specified Tree.

removeViewer(Viewer3D) - Static method in class sc.fiji.snt.SNTUtils

removeWarningListener(PlausibilityMonitor.WarningListener) - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

removeZigzags(DirectedWeightedGraph) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Removes zigzag artifacts from the graph.

render(Collection<Tree>, String) - Static method in class sc.fiji.snt.gui.cmds.FigCreatorCmd

Convenience method to quickly display a collection of Trees

renderedWidth(String) - Static method in class sc.fiji.snt.gui.GuiUtils

renderFrames(List<Bvv.Keyframe>, String) - Method in class sc.fiji.snt.viewer.Bvv

Renders an animation between a list of keyframes, saving each frame as a PNG screenshot.

renderQuick() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

repaint() - Method in class sc.fiji.snt.viewer.Bvv

Forces a repaint of the viewer, updating volume renderings but not overlays.

repaintAllPanes() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

repaintTree() - Method in class sc.fiji.snt.gui.OntologyBrowser.OntologyTab

Triggers a repaint on the tree (e.g., after external state changes that affect the cell renderer).

REPEAT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

replace(String, double, double) - Method in class sc.fiji.snt.analysis.SNTTable

replace(SNTChart) - Method in class sc.fiji.snt.analysis.SNTChart

Replaces the current chart with the specified instance

replaceAll(Collection<? extends SeedPoint>) - Method in class sc.fiji.snt.seed.SeedOverlay

Replaces the current contents with the given seeds.

replaceAll(List<Path>) - Method in class sc.fiji.snt.Tree

Replaces all Paths in this Tree.

replaceAllAt(Map<Integer, SeedPoint>) - Method in class sc.fiji.snt.seed.SeedOverlay

Bulk-replaces seeds at multiple positions, firing listeners and invalidating the spatial index once at the end.

replaceAt(int, SeedPoint) - Method in class sc.fiji.snt.seed.SeedOverlay

Replaces the seed at the given index.

replaceCurrentPath(Path) - Method in class sc.fiji.snt.SNT

replaceGraph(AnnotationGraphAdapter, boolean) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphComponent

replaceLegend(JFreeChart, XYPlot, LegendItemCollection) - Static method in class sc.fiji.snt.analysis.AnalysisUtils

Add a custom legend showing phase types and their colors.

replaceNodes(Path) - Method in class sc.fiji.snt.Path

Replaces all nodes of this path with those from the replacement path, preserving hierarchical relationships (parent, children, connections).

replaceNodesWithFittedVersion() - Method in class sc.fiji.snt.Path

Report(List<PolarProfileStats.PolarPeak>, List<PolarProfileStats.PolarPeak>, double, double, double, double, CircularModels.VonMisesFit, CircularModels.VonMisesFit) - Constructor for record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.Report

Creates an instance of a Report record class.

reportEveryMilliseconds - Variable in class sc.fiji.snt.tracing.AbstractSearch

reportFinished(boolean) - Method in class sc.fiji.snt.tracing.BiSearch

reportFinished(boolean) - Method in class sc.fiji.snt.tracing.FillerThread

reportFinished(boolean) - Method in class sc.fiji.snt.tracing.SearchThread

reportFinished(boolean) - Method in class sc.fiji.snt.tracing.TubularGeodesicsTracer

reportPointsInSearch() - Method in class sc.fiji.snt.tracing.AbstractSearch

reportPointsInSearch() - Method in class sc.fiji.snt.tracing.BiSearch

reportPointsInSearch() - Method in class sc.fiji.snt.tracing.FillerThread

reportPointsInSearch() - Method in class sc.fiji.snt.tracing.SearchThread

reportProgress(float) - Method in class sc.fiji.snt.tracing.TubularGeodesicsTracer

requestStop() - Method in class sc.fiji.snt.tracing.TubularGeodesicsTracer

requireShiftToFork - Variable in class sc.fiji.snt.SNT

requireVersion(String) - Method in class sc.fiji.snt.SNTService

Ensures the running SNT version meets a minimum requirement.

resampleCurve(DirectedWeightedGraph, double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Resamples the curve to have evenly spaced points.

resampleEnabled - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

resampleStep - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

reset() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

reset() - Method in class sc.fiji.snt.BookmarkManager

Clears all bookmarks.

reset() - Method in class sc.fiji.snt.DelineationsManager

Deletes all delineations.

reset() - Method in class sc.fiji.snt.gui.cmds.PrefsCmd

reset() - Method in class sc.fiji.snt.gui.FileChooser

Resets preferences, column widths (detailed view), list of recent locations, and pattern filters.

reset() - Method in class sc.fiji.snt.gui.ScriptRecorder

reset() - Method in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

reset() - Method in class sc.fiji.snt.SNTUI

reset() - Method in class sc.fiji.snt.util.BoundingBox

reset() - Method in class sc.fiji.snt.util.CircleCursor3D

reset() - Method in class sc.fiji.snt.util.DiskCursor3D

reset() - Method in class sc.fiji.snt.util.PathCursor

resetAndResizeColumnsMenuItem(JTable, Runnable, float...) - Static method in class sc.fiji.snt.gui.GuiUtils.JTables

"Resize/Reset Columns" menu item that restores model column order and then applies width fractions.

resetBackBuffer() - Method in class sc.fiji.snt.TracerCanvas

resetColor() - Method in class sc.fiji.snt.Path

Resets this path color, forcing SNT to render it under default settings.

resetColumnOrder(JTable) - Static method in class sc.fiji.snt.gui.GuiUtils.JTables

Restores the table's column order to match the model order (in case the user dragged columns around).

resetEdges - Variable in class sc.fiji.snt.gui.cmds.mxOrganicLayoutPrefsCmd

Specifies if all edge points of traversed edges should be removed.

resetFor(ImagePlus) - Method in class sc.fiji.snt.gui.GuiUtils.JTables.VisitingZoom

Resets the percentage to roughly two zoom steps above the image canvas's current magnification, or 600% when imp == null or has no canvas yet.

resetFrameLocation() - Static method in class sc.fiji.snt.gui.cmds.ShortcutWindowCmd

resetIDs() - Method in class sc.fiji.snt.PathAndFillManager

resetListeners(Path) - Method in class sc.fiji.snt.PathAndFillManager

resetListeners(Path, boolean) - Method in class sc.fiji.snt.PathAndFillManager

resetMinMax() - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

resetOptions() - Method in class sc.fiji.snt.SNTPrefs

resetPreferences() - Static method in class sc.fiji.snt.gui.FileChooser

Resets persisting preferences, including list of recent locations.

resetRegression() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

resetRestrictions() - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

resetRestrictions() - Method in class sc.fiji.snt.analysis.TreeStatistics

Removes any filtering restrictions that may have been set.

resetSpatialSettings(boolean) - Method in class sc.fiji.snt.PathAndFillManager

resetState() - Method in class sc.fiji.snt.SNTUI

resetUI() - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

resetUI() - Method in class sc.fiji.snt.io.WekaModelLoader

resetUI(boolean) - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

resetUI(boolean) - Method in class sc.fiji.snt.gui.cmds.ComputeSecondaryImg

resetUI(boolean, int) - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

resetView() - Method in class sc.fiji.snt.viewer.Bvv

Resets the viewer to a fit-to-viewport transform, centering the loaded volume in the canvas.

resetView() - Method in class sc.fiji.snt.viewer.Viewer3D

Resets the view to its default position and orientation.

RESIZE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

RESIZE_REQUIRED - Static variable in class sc.fiji.snt.SNTPrefs

resizeColumns(JTable, float...) - Static method in class sc.fiji.snt.gui.GuiUtils.JTables

Applies a sequence of preferred column widths to the table, each expressed as a fraction of the current total column width.

resolvePathToSource(String) - Static method in class sc.fiji.snt.io.SpimDataUtils

Resolves a file path to either an AbstractSpimData (for .ims and .xml files) or an ImgPlus (fallback).

resolveSpacing(RandomAccessibleInterval<?>, double[]) - Static method in class sc.fiji.snt.util.ImgUtils

Resolves pixel spacing for a RandomAccessibleInterval.

RESTORE_LOADED_IMGS - Static variable in class sc.fiji.snt.SNTPrefs

restoreDefaultCursor() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

restoreLookAndFeel() - Static method in class sc.fiji.snt.gui.GuiUtils

RestoreSessionCmd - Class in sc.fiji.snt.gui.cmds

Restores a tracing session including traces, bookmarks, and notes.

RestoreSessionCmd() - Constructor for class sc.fiji.snt.gui.cmds.RestoreSessionCmd

restrictRegToPercentile(double, double) - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

restrictRegToRange(double, double) - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

restrictToSubset(int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.TabularParser

restrictToSWCType(int...) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

restrictToSWCType(int...) - Method in class sc.fiji.snt.analysis.TreeStatistics

Restricts analysis to Paths sharing the specified SWC flag(s).

result - Variable in class sc.fiji.snt.tracing.BiSearch

RETRACTION - Enum constant in enum class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhaseType

Retraction phase - negative growth

RetractionEvent(int, int, double, double, double, double, double, double, double) - Constructor for record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.RetractionEvent

Creates an instance of a RetractionEvent record class.

reveal(File) - Static method in class sc.fiji.snt.gui.FileChooser

Reveals the specified file in the native file explorer.

reverse() - Method in class sc.fiji.snt.Path

Reverses this path so that its starting node becomes the last and vice versa.

reversed() - Method in class sc.fiji.snt.Path

reviewed() - Method in record class sc.fiji.snt.analysis.curation.CurationTags.Partition

Paths with any review status (i.e. any cur:* tag).

RIGHT_HEMISPHERE - Static variable in interface sc.fiji.snt.annotation.BrainAnnotation

Character constant representing the right hemisphere

ringPlot(String, HashMap<String, Double>, HashMap<String, Color>) - Static method in class sc.fiji.snt.analysis.AnalysisUtils

Generates a ring plot (aka donut plot).

ringPlot(String, HashMap<GrowthAnalyzer.GrowthPhaseType, Double>) - Static method in class sc.fiji.snt.analysis.AnalysisUtils

Creates a ring plot of growth phases.

ROBOT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

ROCKET - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

ROI_AUTO_DETECT - Static variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

ROI_CENTROID - Static variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

ROI_CENTROID - Static variable in interface sc.fiji.snt.tracing.auto.AutoTracer

Rooting strategy: A single tree is created with all branches connected to the geometric centroid of the soma ROI.

ROI_CENTROID_WEIGHTED - Static variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

ROI_CENTROID_WEIGHTED - Static variable in interface sc.fiji.snt.tracing.auto.AutoTracer

Rooting strategy: A single tree is created with all branches connected to a weighted centroid computed from nodes inside the soma ROI.

ROI_CONTAINED - Static variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

ROI_CONTAINED - Static variable in interface sc.fiji.snt.tracing.auto.AutoTracer

Rooting strategy: Trees are rooted on nodes contained within the soma ROI.

ROI_EDGE - Static variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

ROI_EDGE - Static variable in interface sc.fiji.snt.tracing.auto.AutoTracer

Rooting strategy: Separate trees are created for each neurite exiting the soma ROI.

ROI_UNSET - Static variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

ROI_UNSET - Static variable in interface sc.fiji.snt.tracing.auto.AutoTracer

Rooting strategy: Tree is rooted at an algorithm-specific point (e.g., seed point for grayscale tracers, arbitrary endpoint for binary tracers).

RoiConverter - Class in sc.fiji.snt.analysis

Converts SNT Paths into (IJ1) ROIs.

RoiConverter(Collection<Path>, ImagePlus) - Constructor for class sc.fiji.snt.analysis.RoiConverter

Instantiates a new Converter.

RoiConverter(Path, ImagePlus) - Constructor for class sc.fiji.snt.analysis.RoiConverter

Instantiates a new Converter.

RoiConverter(Tree) - Constructor for class sc.fiji.snt.analysis.RoiConverter

Instantiates a new Converter.

RoiConverter(Tree, ImagePlus) - Constructor for class sc.fiji.snt.analysis.RoiConverter

Instantiates a new Converter.

ROIExporterCmd - Class in sc.fiji.snt.plugin

Command providing a GUI for RoiConverter and allowing export of Paths to the IJ1 ROI Manager.

ROIExporterCmd() - Constructor for class sc.fiji.snt.plugin.ROIExporterCmd

roiPlane - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

roiToSomaPath(Roi, double[]) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Creates a single-node soma Path from an ImageJ ROI.

roiToSomaPath(Roi, Path) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Creates a single-node soma Path from an ImageJ ROI using calibration from a reference Path.

ROOT - Enum constant in enum class sc.fiji.snt.tracing.auto.AutoTracer.SeedRole

Starting point: tree grows outward from here.

ROOT_ANGLE_B_FACTOR - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Root angles: Balancing factor

ROOT_ANGLE_C_BIAS - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Root angles: Centripetal bias

ROOT_ANGLE_M_DIRECTION - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Root angles: Mean direction

ROOT_NODES_ANY - Static variable in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

Flag for defining the profile center as the average position of root nodes of all primary Paths.

ROOT_NODES_APICAL_DENDRITE - Static variable in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

Flag for defining the profile center as the average position of root nodes of Paths tagged as Apical Dendrite.

ROOT_NODES_AXON - Static variable in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

Flag for defining the profile center as the average position of root nodes of Paths tagged as Axon.

ROOT_NODES_CUSTOM - Static variable in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

Flag for defining the profile center as the average position of root nodes of Paths tagged as Custom.

ROOT_NODES_DENDRITE - Static variable in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

Flag for defining the profile center as the average position of root nodes of Paths tagged as (Basal) Dendrite

ROOT_NODES_SOMA - Static variable in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

Flag for defining the profile center as the average position of root nodes of primary Paths tagged as Soma

ROOT_NODES_SOMA_ANY - Static variable in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

Flag for defining the profile center as the average position of root nodes of _ANY_ Paths tagged as Soma, independently of connectivity

ROOT_NODES_UNDEFINED - Static variable in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

Flag for defining the profile center as the average position of root nodes of Paths tagged as Undefined

rootAngleAnalysis() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

RootAngleAnalyzer - Class in sc.fiji.snt.analysis

Class to perform Root angle analysis on a Tree according to Bird and Cuntz 2019, PMID 31167149.

RootAngleAnalyzer(Tree) - Constructor for class sc.fiji.snt.analysis.RootAngleAnalyzer

Constructs a RootAngleAnalyzer for the given tree.

RootAngleAnalyzerCmd - Class in sc.fiji.snt.plugin

Command to perform Root angle analysis on a collection of Trees

RootAngleAnalyzerCmd() - Constructor for class sc.fiji.snt.plugin.RootAngleAnalyzerCmd

Instantiates a new RootAngleAnalyzerCmd.

RootAngleAnalyzerCmd(Collection<Tree>) - Constructor for class sc.fiji.snt.plugin.RootAngleAnalyzerCmd

Instantiates a new RootAngleAnalyzerCmd.

RootAngleAnalyzerCmd(Tree) - Constructor for class sc.fiji.snt.plugin.RootAngleAnalyzerCmd

Instantiates a new RootAngleAnalyzerCmd for a single Tree

rootChoice - Variable in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

rootStrategy - Variable in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

rotate(float) - Method in class sc.fiji.snt.viewer.Viewer3D

Rotates the scene.

rotate(int, double) - Method in class sc.fiji.snt.Tree

Rotates the tree.

rotate90(ImagePlus, String) - Static method in class sc.fiji.snt.util.ImpUtils

Rotates an image 90 degrees.

ROUNDNESS - Static variable in class sc.fiji.snt.analysis.ConvexHullAnalyzer

roundPos(double[], long[]) - Method in class sc.fiji.snt.util.CircleCursor3D

ROUTE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

rubberband - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor

rubberBandTracing - Variable in class sc.fiji.snt.SNT

RULER - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

RULER_VERTICAL - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

run() - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

run() - Method in class sc.fiji.snt.analysis.NodeProfiler

run() - Method in class sc.fiji.snt.analysis.PathProfiler

run() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

run() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

run() - Method in class sc.fiji.snt.analysis.sholl.math.Comparator

run() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

run() - Method in class sc.fiji.snt.analysis.TreeStatistics

Generates detailed summaries in which measurements are grouped by SWC-type flags

run() - Method in class sc.fiji.snt.filter.Frangi

run() - Method in class sc.fiji.snt.filter.SpectralSimilarity

run() - Method in class sc.fiji.snt.filter.Tubeness

run() - Method in class sc.fiji.snt.gui.cmds.AddTextAnnotationCmd

run() - Method in class sc.fiji.snt.gui.cmds.AlongPathDetectorCmd

run() - Method in class sc.fiji.snt.gui.cmds.AnnotationGraphGeneratorCmd

run() - Method in class sc.fiji.snt.gui.cmds.AnnotationGraphRecViewerCmd

run() - Method in class sc.fiji.snt.gui.cmds.BackupManagerCmd

run() - Method in class sc.fiji.snt.gui.cmds.BvvCmd

run() - Method in class sc.fiji.snt.gui.cmds.BvvRenderingOptionsCmd

run() - Method in class sc.fiji.snt.gui.cmds.ChooseDatasetCmd

run() - Method in class sc.fiji.snt.gui.cmds.ColorMapReconstructionCmd

run() - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

run() - Method in class sc.fiji.snt.gui.cmds.CompareFilesCmd

run() - Method in class sc.fiji.snt.gui.cmds.ComputeSecondaryImg

run() - Method in class sc.fiji.snt.gui.cmds.CostFunctionSelectionCmd

run() - Method in class sc.fiji.snt.gui.cmds.CustomizeAxesCmd

run() - Method in class sc.fiji.snt.gui.cmds.CustomizeLegendCmd

run() - Method in class sc.fiji.snt.gui.cmds.CustomizeObjCmd

run() - Method in class sc.fiji.snt.gui.cmds.CustomizeTreeCmd

run() - Method in class sc.fiji.snt.gui.cmds.DistributionBPCmd

run() - Method in class sc.fiji.snt.gui.cmds.DistributionCPCmd

run() - Method in class sc.fiji.snt.gui.cmds.DuplicateCmd

run() - Method in class sc.fiji.snt.gui.cmds.EnableSciViewUpdateSiteCmd

run() - Method in class sc.fiji.snt.gui.cmds.FigCreatorCmd

run() - Method in class sc.fiji.snt.gui.cmds.FilterOrTagPathsByAngleCmd

run() - Method in class sc.fiji.snt.gui.cmds.GraphGeneratorCmd

run() - Method in class sc.fiji.snt.gui.cmds.ImportSeedPointsCmd

run() - Method in class sc.fiji.snt.gui.cmds.InsectBrainImporterCmd

run() - Method in class sc.fiji.snt.gui.cmds.JSONImporterCmd

run() - Method in class sc.fiji.snt.gui.cmds.LabelProximityDetectorCmd

run() - Method in class sc.fiji.snt.gui.cmds.LoadObjCmd

run() - Method in class sc.fiji.snt.gui.cmds.LoadReconstructionCmd

run() - Method in class sc.fiji.snt.gui.cmds.LoadSeedsFromLabelsImageCmd

run() - Method in class sc.fiji.snt.gui.cmds.LoadSeedsFromROIsCmd

run() - Method in class sc.fiji.snt.gui.cmds.MLImporterCmd

run() - Method in class sc.fiji.snt.gui.cmds.MultiSpectralRefinerCmd

run() - Method in class sc.fiji.snt.gui.cmds.MultiSWCImporterCmd

run() - Method in class sc.fiji.snt.gui.cmds.mxCircleLayoutGroupedCmd

run() - Method in class sc.fiji.snt.gui.cmds.mxOrganicLayoutPrefsCmd

run() - Method in class sc.fiji.snt.gui.cmds.NDFImporterCmd

run() - Method in class sc.fiji.snt.gui.cmds.NewGraphOptionsCmd

run() - Method in class sc.fiji.snt.gui.cmds.OpenDatasetCmd

run() - Method in class sc.fiji.snt.gui.cmds.PathFitterCmd

run() - Method in class sc.fiji.snt.gui.cmds.PeripathDetectorCmd

run() - Method in class sc.fiji.snt.gui.cmds.PersistenceAnalyzerCmd

run() - Method in class sc.fiji.snt.gui.cmds.PrefsCmd

run() - Method in class sc.fiji.snt.gui.cmds.ReconstructionViewerCmd

run() - Method in class sc.fiji.snt.gui.cmds.RecViewerPrefsCmd

run() - Method in class sc.fiji.snt.gui.cmds.RemoteSWCImporterCmd

run() - Method in class sc.fiji.snt.gui.cmds.RestoreSessionCmd

run() - Method in class sc.fiji.snt.gui.cmds.SaveMeasurementsCmd

run() - Method in class sc.fiji.snt.gui.cmds.SaveSessionCmd

run() - Method in class sc.fiji.snt.gui.cmds.ShortcutWindowCmd

run() - Method in class sc.fiji.snt.gui.cmds.ShowCorrespondencesCmd

run() - Method in class sc.fiji.snt.gui.cmds.SNTLoaderCmd

run() - Method in class sc.fiji.snt.gui.cmds.SpotSpineLoaderCmd

run() - Method in class sc.fiji.snt.gui.cmds.SWCTypeFilterCmd

run() - Method in class sc.fiji.snt.gui.cmds.SWCTypeOptionsCmd

run() - Method in class sc.fiji.snt.gui.cmds.TranslateReconstructionsCmd

run() - Method in class sc.fiji.snt.gui.cmds.TreeGraphRecViewerCmd

run() - Method in class sc.fiji.snt.gui.cmds.TwoDHistCmd

run() - Method in class sc.fiji.snt.gui.CostPalette

run() - Method in class sc.fiji.snt.gui.SigmaPalette

run() - Method in class sc.fiji.snt.io.WekaModelLoader

run() - Method in class sc.fiji.snt.plugin.AnalyzerCmd

Deprecated.

run() - Method in class sc.fiji.snt.plugin.AnnotationDensityCmd

run() - Method in class sc.fiji.snt.plugin.AutotraceFromBinarySeedsCmd

run() - Method in class sc.fiji.snt.plugin.AutotraceFromBinaryTipsCmd

run() - Method in class sc.fiji.snt.plugin.AutotraceFromSeedsCmd

run() - Method in class sc.fiji.snt.plugin.AutotraceFromTipsCmd

run() - Method in class sc.fiji.snt.plugin.AutotraceFromWaypointsCmd

run() - Method in class sc.fiji.snt.plugin.BinaryTracerCmd

run() - Method in class sc.fiji.snt.plugin.BinaryTracerFileCmd

run() - Method in class sc.fiji.snt.plugin.BrainAnnotationCmd

run() - Method in class sc.fiji.snt.plugin.ChooseDataset

run() - Method in class sc.fiji.snt.plugin.ConvexHullCmd

run() - Method in class sc.fiji.snt.plugin.GraphAdapterMapperCmd

run() - Method in class sc.fiji.snt.plugin.GroupAnalyzerCmd

run() - Method in class sc.fiji.snt.plugin.GrowthAnalyzerCmd

run() - Method in class sc.fiji.snt.plugin.GWDTMultiSomaCmd

run() - Method in class sc.fiji.snt.plugin.GWDTMultiSomaFileCmd

run() - Method in class sc.fiji.snt.plugin.GWDTTracerCmd

run() - Method in class sc.fiji.snt.plugin.GWDTTracerFileCmd

run() - Method in class sc.fiji.snt.plugin.InterpolateRadiiCmd

run() - Method in class sc.fiji.snt.plugin.LabkitLoaderCmd

run() - Method in class sc.fiji.snt.plugin.LocalThicknessCmd

run() - Method in class sc.fiji.snt.plugin.PathAnalyzerCmd

run() - Method in class sc.fiji.snt.plugin.PathMatcherCmd

run() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd

run() - Method in class sc.fiji.snt.plugin.PathSpineAnalysisCmd

run() - Method in class sc.fiji.snt.plugin.PathTimeAnalysisCmd

run() - Method in class sc.fiji.snt.plugin.PlotterCmd

run() - Method in class sc.fiji.snt.plugin.ROIExporterCmd

run() - Method in class sc.fiji.snt.plugin.RootAngleAnalyzerCmd

run() - Method in class sc.fiji.snt.plugin.ShollAnalysisBulkTreeCmd

run() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCmd

run() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCommonCmd

run() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgInteractiveCmd

run() - Method in class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

run() - Method in class sc.fiji.snt.plugin.ShollAnalysisTreeCmd

run() - Method in class sc.fiji.snt.plugin.ShollAnalysisTreeInteractiveCmd

run() - Method in class sc.fiji.snt.plugin.SkeletonizerCmd

run() - Method in class sc.fiji.snt.plugin.SomaDetectorCmd

run() - Method in class sc.fiji.snt.plugin.StrahlerCmd

run() - Method in class sc.fiji.snt.plugin.TreeMapperCmd

run() - Method in class sc.fiji.snt.plugin.TWSLoaderCmd

run() - Method in class sc.fiji.snt.tracing.BiSearch

run() - Method in class sc.fiji.snt.tracing.FillerThread

run() - Method in class sc.fiji.snt.tracing.ManualTracerThread

run() - Method in class sc.fiji.snt.tracing.SearchThread

run() - Method in class sc.fiji.snt.tracing.TubularGeodesicsTracer

run() - Method in class sc.fiji.snt.util.PointDeduplicator

Runs the greedy NMS.

run(ImageProcessor) - Method in class sc.fiji.snt.plugin.ij1.SummarizeSkeleton

run(String) - Method in class sc.fiji.snt.gui.cmds.ShortcutWindowCmd

run(String) - Method in class sc.fiji.snt.plugin.ij1.Strahler

This method is called when the plugin is loaded.

run(String) - Method in class sc.fiji.snt.util.LSystemsTree

run(RandomAccessibleInterval<U>) - Method in class sc.fiji.snt.filter.Frangi

run(RandomAccessibleInterval<U>) - Method in class sc.fiji.snt.filter.SpectralSimilarity

run(RandomAccessibleInterval<U>) - Method in class sc.fiji.snt.filter.Tubeness

runAnalysis() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCommonCmd

runAnalysis() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgInteractiveCmd

runAnalysis() - Method in class sc.fiji.snt.plugin.ShollAnalysisTreeInteractiveCmd

runAutotracingWizard() - Method in class sc.fiji.snt.SNTUI

Launches the autotracing wizard for the active image.

runCommand() - Method in class sc.fiji.snt.plugin.AutotraceFromBinarySeedsCmd

runCommand() - Method in class sc.fiji.snt.plugin.AutotraceFromBinaryTipsCmd

runCommand() - Method in class sc.fiji.snt.plugin.AutotraceFromSeedsCmd

runCommand() - Method in class sc.fiji.snt.plugin.AutotraceFromTipsCmd

runCommand() - Method in class sc.fiji.snt.plugin.AutotraceFromWaypointsCmd

runCommand() - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

Executes the core tracing pipeline: loads images (from file or choice widgets based on BinaryTracerCommonCmd.isFileMode()), validates inputs, runs BinaryTracer, and post-processes the resulting trees.

runCommand() - Method in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

runCommand(Class<? extends Command>, HashMap<String, Object>) - Method in class sc.fiji.snt.SNTUI

Runs a Scijava command associated with SNT.

runCommand(String) - Method in class sc.fiji.snt.gui.SNTCommandFinder

runCommand(String) - Method in class sc.fiji.snt.PathManagerUI

Runs a menu command.

runCommand(String) - Method in class sc.fiji.snt.SNTUI

Runs a menu command (as listed in the menu bar hierarchy).

runCommand(String) - Method in class sc.fiji.snt.viewer.Viewer3D

runCommand(String, String...) - Method in class sc.fiji.snt.PathManagerUI

Runs a menu command with options.

runCommand(String, String...) - Method in class sc.fiji.snt.SNTUI

Runs a menu command with options.

runCustomCommand(String) - Method in class sc.fiji.snt.PathManagerUI

runCustomCommand(String) - Method in class sc.fiji.snt.SNTUI

runDeepScan(Collection<Path>) - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

Runs all enabled PlausibilityCheck.DeepChecks against the given paths.

runFastMarching(double, long) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Initializes storage and runs Fast Marching from the given seed.

runFullScan(Collection<Path>) - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

Runs all enabled checks (both live and deep) against the given paths.

runIndices() - Method in class sc.fiji.snt.util.PointDeduplicator

Runs the greedy NMS and returns the original indices of surviving points.

runMultiSoma() - Method in class sc.fiji.snt.plugin.GWDTMultiSomaCommonCmd

running - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

RUNNING_CMD - Static variable in class sc.fiji.snt.SNTUI

runScript(String) - Static method in class sc.fiji.snt.gui.ScriptInstaller

Runs the specified script known to ScriptService.

runScript(String, String) - Method in class sc.fiji.snt.gui.ScriptInstaller

runScript(String, String, Map<String, Object>) - Static method in class sc.fiji.snt.gui.ScriptInstaller

runSecondaryLayerWizard() - Method in class sc.fiji.snt.SNTUI

Runs the 'secondary layer' wizard prompt for built-in filters

runSecondaryLayerWizard(String, double[]) - Method in class sc.fiji.snt.SNTUI

Runs the 'secondary layer wizard' in the background, without displaying prompt.

runSNTCommandFinderCommand(String) - Method in class sc.fiji.snt.SNTUI

S

S_SHELL - Static variable in interface sc.fiji.snt.analysis.sholl.math.ShollStats

Flag for spherical shell normalization (Semi-log/Log-log method)

SAME - Enum constant in enum class sc.fiji.snt.FillConverter.ResultType

sameCalibration(ImagePlus, ImagePlus) - Static method in class sc.fiji.snt.util.ImpUtils

sameCTDimensions(ImagePlus, ImagePlus) - Static method in class sc.fiji.snt.util.ImpUtils

sameCTOnly(boolean) - Method in class sc.fiji.snt.util.CrossoverFinder.Config

Sets CrossoverFinder.Config.sameCTOnly.

sameXYZDimensions(ImagePlus, ImagePlus) - Static method in class sc.fiji.snt.util.ImpUtils

sampleCrossSection(int, double, double, double, double, double, double[], double[], double, double, double, RealRandomAccess<FloatType>) - Static method in class sc.fiji.snt.tracing.CrossSectionUtils

Samples a square cross-section of an image on the plane perpendicular to a path tangent at a given node position.

sampleDistances(Collection<Path>, Img<FloatType>) - Static method in class sc.fiji.snt.analysis.detection.DetectorUtils

Samples the EDT at every node position of the given paths.

sampleDistancesWithIndices(Path, Img<FloatType>) - Static method in class sc.fiji.snt.analysis.detection.DetectorUtils

Samples the EDT at each node of a single path, returning the distance value and node index for each in-bounds node.

sampleImage() - Static method in class sc.fiji.snt.analysis.sholl.ShollUtils

Returns the plugin's sample image (File>Samples>ddaC Neuron).

sampleProfile(int, double, double, double, double[], double, double, RealRandomAccess<FloatType>) - Static method in class sc.fiji.snt.tracing.CrossSectionUtils

Samples a 1D intensity profile along a direction vector, centered on a given world position.

sampleSize() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCalibrator.CheckSummary

Returns the value of the sampleSize record component.

sampleTree() - Method in class sc.fiji.snt.util.LSystemsTree

Creates a simple fractal tree.

sanitizedUnit(String) - Static method in class sc.fiji.snt.util.BoundingBox

sanitizeRadii(boolean) - Method in class sc.fiji.snt.Path

Sanitizes node radii by interpolating invalid values (zero, NaN, or negative).

sanitizeRadii(double, double, boolean) - Method in class sc.fiji.snt.Path

Sanitizes node radii by enforcing bounds and interpolating outliers.

sanitizeRadii(DoublePredicate, boolean) - Method in class sc.fiji.snt.Path

Sanitizes node radii by interpolating values that match the given predicate.

save(ImagePlus, String) - Static method in class sc.fiji.snt.util.ImpUtils

Saves the specified image.

save(File) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

save(File) - Method in class sc.fiji.snt.analysis.SNTChart

Saves this chart.

save(File) - Method in class sc.fiji.snt.analysis.SNTTable

save(File) - Method in class sc.fiji.snt.BookmarkManager

Saves bookmarks to the specified file.

save(File) - Method in class sc.fiji.snt.io.MouseLightLoader

Convenience method to save JSON data.

save(File) - Method in class sc.fiji.snt.NotesUI

save(String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

save(String) - Method in class sc.fiji.snt.analysis.SNTTable

save(String) - Method in class sc.fiji.snt.BookmarkManager

save(String) - Method in class sc.fiji.snt.io.MouseLightLoader

Convenience method to save JSON data.

save(String) - Method in class sc.fiji.snt.SNTService

Saves all the existing paths to a file.

save(String) - Method in class sc.fiji.snt.Tree

Saves this Tree to a .TRACES (XML, compressed) file.

save(String) - Method in class sc.fiji.snt.viewer.MultiViewer2D

save(String, double) - Method in class sc.fiji.snt.analysis.SNTChart

Saves this chart.

save(Supplier<SNTTable>, JTable) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

save(RandomAccessibleInterval<? extends RealType<?>>, String) - Static method in class sc.fiji.snt.util.ImgUtils

Saves an image to disk as a TIFF file.

save(RandomAccessibleInterval<? extends RealType<?>>, String, T) - Static method in class sc.fiji.snt.util.ImgUtils

Saves an image to disk as a TIFF file, converting pixel values to the specified output type before writing.

save(Table<?, ?>, char, boolean, boolean, File) - Static method in class sc.fiji.snt.analysis.SNTTable

save(PlausibilityMonitor, File, String) - Static method in class sc.fiji.snt.analysis.curation.PlausibilityCalibrator

Saves the current state of a PlausibilityMonitor (thresholds and enabled states) to a .curation properties file.

SAVE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

SAVE_DIALOG - Static variable in class sc.fiji.snt.gui.FilePicker

saveAllPathsToSwc(String) - Method in class sc.fiji.snt.SNTUI

saveAllPathsToSwc(String, String) - Method in class sc.fiji.snt.SNTUI

saveAs(File) - Method in class sc.fiji.snt.seed.SeedOverlay

Writes all held seeds to a CSV file with the canonical header x,y,z,confidence,radius.

saveAsJSON(String) - Method in class sc.fiji.snt.io.MouseLightLoader

Convenience method to save JSON data to a local directory.

saveAsPDF(File, double) - Method in class sc.fiji.snt.analysis.SNTChart

saveAsPDF(String) - Method in class sc.fiji.snt.analysis.SNTChart

saveAsPDF(String, double) - Method in class sc.fiji.snt.analysis.SNTChart

saveAsPNG(File) - Method in class sc.fiji.snt.analysis.SNTChart

saveAsPNG(File, double) - Method in class sc.fiji.snt.analysis.SNTChart

saveAsPNG(String) - Method in class sc.fiji.snt.analysis.SNTChart

saveAsPNG(String, double) - Method in class sc.fiji.snt.analysis.SNTChart

saveAsSVG(File, double) - Method in class sc.fiji.snt.analysis.SNTChart

saveAsSVG(String) - Method in class sc.fiji.snt.analysis.SNTChart

saveAsSVG(String, double) - Method in class sc.fiji.snt.analysis.SNTChart

saveAsSWC(String) - Method in class sc.fiji.snt.io.MouseLightLoader

Convenience method to save SWC data to a local directory.

saveAsSWC(String) - Method in class sc.fiji.snt.Tree

Saves this Tree to an SWC file.

saveDir - Variable in class sc.fiji.snt.viewer.geditor.SNTGraphComponent

saveFile(String, String, String) - Method in class sc.fiji.snt.SNTUI

saveFill() - Method in class sc.fiji.snt.SNT

SaveMeasurementsCmd - Class in sc.fiji.snt.gui.cmds

Saves all open tables, plots, and charts to a specified directory.

SaveMeasurementsCmd() - Constructor for class sc.fiji.snt.gui.cmds.SaveMeasurementsCmd

savePlot(PlotWindow, File, boolean) - Static method in class sc.fiji.snt.gui.cmds.SaveMeasurementsCmd

savePluginPrefs(boolean) - Method in class sc.fiji.snt.SNTPrefs

saveRoisToZip(List<Roi>, File) - Static method in class sc.fiji.snt.analysis.RoiConverter

SaveSessionCmd - Class in sc.fiji.snt.gui.cmds

Saves a tracing session including traces, bookmarks, notes, tables, charts, plots, and RM ROIs.

SaveSessionCmd() - Constructor for class sc.fiji.snt.gui.cmds.SaveSessionCmd

saveSilently(File) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollTable

saveSnapshot() - Method in class sc.fiji.snt.viewer.Viewer3D

Saves a snapshot of current scene as a PNG image.

saveSnapshot(File) - Method in class sc.fiji.snt.viewer.Viewer3D

saveSnapshot(String) - Method in class sc.fiji.snt.viewer.Bvv

Saves a snapshot of current scene as a PNG image to the specified path.

saveSnapshot(String) - Method in class sc.fiji.snt.viewer.Viewer3D

Saves a snapshot of current scene as a PNG image to the specified path.

saveStartupPrefs() - Method in class sc.fiji.snt.SNTPrefs

Deprecated.

saveTablesAndPlots(IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

savetoFileOrFileSeries(File) - Method in class sc.fiji.snt.PathAndFillManager

saveToXML(boolean) - Method in class sc.fiji.snt.SNTUI

saveToXML(File, boolean) - Method in class sc.fiji.snt.SNTUI

saveTracingsAndOpenSiblingImage(boolean) - Method in class sc.fiji.snt.SNTUI

sc.fiji.snt - package sc.fiji.snt

SNT core classes

sc.fiji.snt.analysis - package sc.fiji.snt.analysis

Analysis of Trees.

sc.fiji.snt.analysis.curation - package sc.fiji.snt.analysis.curation

Classes for curation of reconstructions, as implemented by the "Curation Assistant".

sc.fiji.snt.analysis.detection - package sc.fiji.snt.analysis.detection

Feature detectors for traced paths.

sc.fiji.snt.analysis.graph - package sc.fiji.snt.analysis.graph

Classes for handling neuronal reconstructions as graphs

sc.fiji.snt.analysis.growth - package sc.fiji.snt.analysis.growth

Classes for growth analysis of neurites across time

sc.fiji.snt.analysis.sholl - package sc.fiji.snt.analysis.sholl

Sholl analysis of Images, pre-sampled data and Trees.

sc.fiji.snt.analysis.sholl.gui - package sc.fiji.snt.analysis.sholl.gui

GUI customizations (image overlays, plots, etc.) required for Sholl Analysis.

sc.fiji.snt.analysis.sholl.math - package sc.fiji.snt.analysis.sholl.math

Statistical analysis of Sholl data

sc.fiji.snt.analysis.sholl.parsers - package sc.fiji.snt.analysis.sholl.parsers

Parsers to retrieve Sholl profiles from multiple sources (2D/3D images, reconstructions, and tables)

sc.fiji.snt.annotation - package sc.fiji.snt.annotation

Classes handling neuropil annotations and atlases metadata.

sc.fiji.snt.event - package sc.fiji.snt.event

Utilities for TrakEM2 interaction

sc.fiji.snt.filter - package sc.fiji.snt.filter

Filters for detection of tube-like structures

sc.fiji.snt.gui - package sc.fiji.snt.gui

Customizations and commands for SNT's GUI.

sc.fiji.snt.gui.cmds - package sc.fiji.snt.gui.cmds

Scijava-based GUIs for SNT built-in commands.

sc.fiji.snt.hyperpanes - package sc.fiji.snt.hyperpanes

Classes implementing SNT's XY, ZY, and XZ canvases.

sc.fiji.snt.io - package sc.fiji.snt.io

Classes for importing reconstructions into SNT.

sc.fiji.snt.plugin - package sc.fiji.snt.plugin

SNT add-ons as IJ2 commands

sc.fiji.snt.plugin.ij1 - package sc.fiji.snt.plugin.ij1

SNT add-ons as legacy ("IJ1") plugins.

sc.fiji.snt.seed - package sc.fiji.snt.seed

sc.fiji.snt.tracing - package sc.fiji.snt.tracing

Path-finding algorithms for interactive neuron tracing.

sc.fiji.snt.tracing.artist - package sc.fiji.snt.tracing.artist

Artist classes provide visual feedback for tracing algorithm execution.

sc.fiji.snt.tracing.auto - package sc.fiji.snt.tracing.auto

Automatic neuron tracing algorithms that reconstruct complete neuronal morphologies from images without user interaction.

sc.fiji.snt.tracing.auto.gwdt - package sc.fiji.snt.tracing.auto.gwdt

Storage backends for the Gray-Weighted Distance Transform (GWDT) tracing algorithm.

sc.fiji.snt.tracing.cost - package sc.fiji.snt.tracing.cost

Cost function implementations for classes implementing SearchInterface

sc.fiji.snt.tracing.heuristic - package sc.fiji.snt.tracing.heuristic

Heuristic implementations for classes implementing SearchInterface

sc.fiji.snt.tracing.image - package sc.fiji.snt.tracing.image

Data structures used to keep track of encountered nodes during image-based searches for classes implementing SearchInterface

sc.fiji.snt.util - package sc.fiji.snt.util

Miscellaneous SNT utilities, including classes defining reconstruction nodes.

sc.fiji.snt.viewer - package sc.fiji.snt.viewer

Visualization of reconstructions

sc.fiji.snt.viewer.geditor - package sc.fiji.snt.viewer.geditor

Classes implementing SNT's Graph Viewer

scale(double[]) - Method in class sc.fiji.snt.util.BoundingBox

scale(double, double, double) - Method in class sc.fiji.snt.analysis.sholl.Profile

scale(double, double, double) - Method in class sc.fiji.snt.Tree

Scales the tree by the specified factors.

scale(double, double, double) - Method in class sc.fiji.snt.util.PointInImage

Scales this point coordinates.

scale(double, double, double, boolean) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Scales the point coordinates of each vertex by the specified factors.

scale(double, double, double, double) - Method in class sc.fiji.snt.Tree

Scales the tree by the specified factors.

scale(Collection<ShollPoint>, Calibration) - Static method in class sc.fiji.snt.util.ShollPoint

SCALE_BALANCED - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

SCALE_UNBALANCED - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

scaled() - Method in class sc.fiji.snt.analysis.sholl.Profile

scaledMicrometer(double, int) - Static method in class sc.fiji.snt.gui.GuiUtils

Returns a more human-readable representation of a length in micrometers.

scaleEdgeWidths(double, double, String) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter

scan(Collection<Path>) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.DeepCheck

Scans a collection of paths for plausibility issues.

scan(Collection<Path>) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.PathOverlap

scan(Collection<Path>) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.RadiusJumps

scan(Collection<Path>) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.RadiusMonotonicity

scan(Collection<Path>) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.SignalQuality

SCATTER - Static variable in class sc.fiji.snt.viewer.Annotation3D

SCISSORS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

sciViewSNT - Variable in class sc.fiji.snt.SNTUI

SciViewSNT - Class in sc.fiji.snt

Bridges SNT to SciView, allowing Trees to be rendered as scenery objects

SciViewSNT(Context) - Constructor for class sc.fiji.snt.SciViewSNT

Instantiates a new SciViewSNT instance.

SciViewSNT(SNT) - Constructor for class sc.fiji.snt.SciViewSNT

SciViewSNT(SciView) - Constructor for class sc.fiji.snt.SciViewSNT

Instantiates SciViewSNT from an existing SciView instance.

scoreMap - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

scoreMapEnabled - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

scoreMapFilter - Variable in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

scoreMapFilterCallback() - Method in class sc.fiji.snt.plugin.GWDTTracerCommonCmd

Toggles visibility of secondary-image inputs that are only relevant when scoreMapFilter == SCORE_MAP_OTHER.

scoreMapFilterType - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

scoreMapPruneThreshold - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

scoreMapScales - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

ScriptInstaller - Class in sc.fiji.snt.gui

Utility class for discovery of SNT scripts

ScriptInstaller(Context, Component) - Constructor for class sc.fiji.snt.gui.ScriptInstaller

ScriptRecorder - Class in sc.fiji.snt.gui

A dialog for recording SNT operations as scripts in multiple programming languages (BeanShell, Groovy, Python).

ScriptRecorder() - Constructor for class sc.fiji.snt.gui.ScriptRecorder

SCROLL - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

scrollPane(JTable) - Static method in class sc.fiji.snt.gui.GuiUtils.JTables

Wraps a JTable in a JScrollPane with sensible defaults: auto-resize mode set to ALL_COLUMNS, row sorter enabled, and grid lines hidden.

scrollPane(JTable, int, boolean, boolean) - Static method in class sc.fiji.snt.gui.GuiUtils.JTables

Wraps a JTable in a JScrollPane, applying common configuration.

scrollTo(int, int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

scrollToLastRow(JTree) - Static method in class sc.fiji.snt.gui.GuiUtils.JTrees

SD - Enum constant in enum class sc.fiji.snt.analysis.ProfileProcessor.Metric

SEARCH - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

SEARCH_ARROW - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

SEARCH_MINUS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

SEARCH_PLUS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

SearchArtist - Interface in sc.fiji.snt.tracing.artist

Interface for classes that draw the progress of a SearchInterface on a TracerCanvas.

SearchArtistFactory - Class in sc.fiji.snt.tracing.artist

Factory for creation of SearchArtists

SearchArtistFactory() - Constructor for class sc.fiji.snt.tracing.artist.SearchArtistFactory

Constructs a new SearchArtistFactory.

searchArtists - Variable in class sc.fiji.snt.TracerCanvas

SearchField - Class in sc.fiji.snt.gui

An enhanced text field for search operations with built-in options for case-sensitive, word-matching, and regex search modes.

SearchField(String, int) - Constructor for class sc.fiji.snt.gui.SearchField

Constructs a new SearchField with the specified placeholder text and visible buttons.

searchForum(String) - Method in class sc.fiji.snt.gui.GuiUtils

SearchImage<V> - Interface in sc.fiji.snt.tracing.image

General interface for data structures used to keep track of encountered nodes during image-based searches.

SearchImageStack<V> - Class in sc.fiji.snt.tracing.image

A stack of SearchImages, backed by a Int2ObjectOpenHashMap.

SearchImageStack() - Constructor for class sc.fiji.snt.tracing.image.SearchImageStack

SearchImageStack(Supplier<SearchImage<V>>) - Constructor for class sc.fiji.snt.tracing.image.SearchImageStack

searchImageType - Variable in class sc.fiji.snt.SNT

Search Infrastructure - Search tag in package sc.fiji.snt.tracing

Section

SearchInterface - Interface in sc.fiji.snt.tracing

Tracer classes implementing searches between two points should implement this interface.

SearchNode - Interface in sc.fiji.snt.tracing

Interface representing a node in 3D space that can be used in pathfinding and search algorithms.

SearchProgressCallback - Interface in sc.fiji.snt

Callback interface for monitoring progress of a search operation during path tracing.

searchStatus - Variable in class sc.fiji.snt.tracing.DefaultSearchNode

SearchThread - Class in sc.fiji.snt.tracing

Implements a common thread that explores the image using a variety of strategies, e.g., to trace tubular structures or surfaces.

SearchThread(Dataset, boolean, boolean, int, long, SNT.SearchImageType, Cost) - Constructor for class sc.fiji.snt.tracing.SearchThread

SearchThread(RandomAccessibleInterval<? extends RealType<?>>, Calibration, boolean, boolean, int, long, SNT.SearchImageType, Cost) - Constructor for class sc.fiji.snt.tracing.SearchThread

SearchThread(SNT, RandomAccessibleInterval<? extends RealType<?>>, Cost) - Constructor for class sc.fiji.snt.tracing.SearchThread

SearchThreadArtist - Class in sc.fiji.snt.tracing.artist

An artist class responsible for visualizing the progress and state of search threads during path tracing operations.

SearchThreadArtist(SearchThread, Color, Color) - Constructor for class sc.fiji.snt.tracing.artist.SearchThreadArtist

SEC_LAYER_KEY - Static variable in class sc.fiji.snt.gui.cmds.PathFitterCmd

secondaryColor() - Static method in class sc.fiji.snt.gui.IconFactory

secondaryData - Variable in class sc.fiji.snt.SNT

secondaryImageFile - Variable in class sc.fiji.snt.SNT

SEEDLING - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

SeedManager - Class in sc.fiji.snt

Reusable JPanel that controls a SeedOverlay: visibility, LUT, confidence range, transparency, counters, CSV import/export/clear, plus an inline JTable for browsing and editing individual seeds.

SeedManager(SNTUI) - Constructor for class sc.fiji.snt.SeedManager

Creates a panel bound to the given SNT instance's SeedOverlay.

SeedOverlay - Class in sc.fiji.snt.seed

Transient, in-memory store of SeedPoints used to render candidate tracing seeds (e.g., the output of a deep-learning point detector) on SNT's canvas and to feed them to downstream consumers (autotracers, click-to-trace anchors).

SeedOverlay() - Constructor for class sc.fiji.snt.seed.SeedOverlay

SeedOverlay.ColorMode - Enum Class in sc.fiji.snt.seed

How SeedOverlayRenderer should pick each seed's LUT slot.

SeedOverlay.SeedOverlayListener - Interface in sc.fiji.snt.seed

Listener fired on any change to the overlay (add/clear/threshold/visibility).

SeedOverlayCanvasHandler - Class in sc.fiji.snt.seed

Attaches a lightweight MouseListener to a TracerCanvas that lets the user click on a rendered seed (with Alt held) to open the per-seed edit dialog.

seedOverlayChanged(SeedOverlay) - Method in interface sc.fiji.snt.seed.SeedOverlay.SeedOverlayListener

Called after the overlay's contents, threshold, or visibility changed.

SeedOverlayRenderer - Class in sc.fiji.snt

Stateless renderer that draws a SeedOverlay's seeds onto a TracerCanvas's Graphics2D.

SeedPoint - Class in sc.fiji.snt.seed

Immutable candidate seed point used to bootstrap auto-tracing or as a visualization aid for the output of upstream point detectors (e.g., deep-learning probability maps + local-max suppression).

SeedPoint(double, double, double, double, double) - Constructor for class sc.fiji.snt.seed.SeedPoint

Creates a seed without channel/frame assignment and no type/source.

SeedPoint(double, double, double, double, double, int, int) - Constructor for class sc.fiji.snt.seed.SeedPoint

Creates a seed with channel/frame assignment but no type/source.

SeedPoint(double, double, double, double, double, int, int, String, String) - Constructor for class sc.fiji.snt.seed.SeedPoint

Full constructor.

SeedPointEditDialog - Class in sc.fiji.snt.seed

Modal seed editor with two modes: Single: One seed, all nine fields (X, Y, Z, confidence, radius, channel, frame, type, source) are shown and editable; Save rebuilds an immutable SeedPoint and applies it via SeedOverlay.replaceAt(int, SeedPoint); Delete removes the seed.

SeedRois - Class in sc.fiji.snt.seed

Bidirectional SeedPoint-Roi converter.

SeedTableModel - Class in sc.fiji.snt.seed

TableModel backed by a SeedOverlay.

SeedTableModel(SeedOverlay) - Constructor for class sc.fiji.snt.seed.SeedTableModel

Builds a model without the Status column.

SeedTableModel(SeedOverlay, SNT) - Constructor for class sc.fiji.snt.seed.SeedTableModel

Builds a model with an optional Status column.

seedVoxel - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

select(Path) - Method in class sc.fiji.snt.PathManagerUI

Selects a specific path in the Path Manager.

selectAll() - Method in class sc.fiji.snt.PathManagerUI

Selects all paths.

selectColor(Color) - Method in class sc.fiji.snt.gui.ColorMenu

selectedColor - Variable in class sc.fiji.snt.SNT

selectedColor() - Static method in class sc.fiji.snt.gui.IconFactory

selectedColor3f - Variable in class sc.fiji.snt.SNT

selectionExists() - Method in class sc.fiji.snt.PathManagerUI

selectNone() - Method in class sc.fiji.snt.gui.ColorMenu

selectPath(Path, boolean) - Method in class sc.fiji.snt.SNT

selectSWCColor(SNTColor) - Method in class sc.fiji.snt.gui.ColorMenu

selectTab(String) - Method in class sc.fiji.snt.SNTUI

Activates the specified tab.

selectTopSomasByThickness(List<SomaUtils.SomaResult>, RandomAccessibleInterval<T>, int) - Static method in class sc.fiji.snt.tracing.auto.SomaUtils

Selects the top-N somas by EDT thickness (distance to nearest background pixel at each soma's center), ranking by descending EDT value.

SEMI_LOG - Static variable in interface sc.fiji.snt.analysis.sholl.math.ShollStats

Flag for imposing Semi-log analysis

SEND_TO_TRAKEM2 - Static variable in class sc.fiji.snt.event.SNTEvent

Event type indicating data should be sent to TrakEM2

SEPARATOR - Static variable in class sc.fiji.snt.gui.OntologyBrowser

Separator used for serializing hierarchical paths.

serializePath(TreePath) - Static method in class sc.fiji.snt.gui.OntologyBrowser

Serializes a TreePath as a "::"-delimited string, excluding the root node.

set(int, int, Object) - Method in class sc.fiji.snt.analysis.SNTTable

set(String, boolean) - Method in class sc.fiji.snt.SNTPrefs

Sets a boolean preference value.

set(String, int, Object) - Method in class sc.fiji.snt.analysis.SNTTable

set(String, String) - Method in class sc.fiji.snt.SNTPrefs

Sets a string preference value.

set(String, String, Object) - Method in class sc.fiji.snt.analysis.SNTTable

set2DDisplayCanvas(boolean) - Method in class sc.fiji.snt.SNTPrefs

Sets whether to force 2D display canvas.

set3DUniverse(Image3DUniverse) - Method in class sc.fiji.snt.SNT

set3DViewerResamplingFactor(int) - Method in class sc.fiji.snt.SNTPrefs

setAbsoluteWindowSize(int) - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Sets the absolute window size for change point detection in frames.

setAccel(String) - Method in class sc.fiji.snt.viewer.Bvv.Keyframe

Sets the easing type by name.

setAcronym(String) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

setActive(boolean) - Method in class sc.fiji.snt.viewer.BvvMultiSource

Sets the active/visible state for all sources in the group.

setAggressiveSpikeSuppression(boolean) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D

Sets experimental spike suppression mode.

setAliases(String[]) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

setAllowVoxelGap(boolean) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets whether to allow bridging single-voxel intensity gaps during fast marching.

setAlternateShells() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

setAlternateShells(Color, Color) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

setAnalysisScope() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCommonCmd

setAnatomicalMapping(String) - Method in class sc.fiji.snt.viewer.Viewer3D

Applies the anatomical axis mapping associated with a known reference brain.

setAnatomicalMapping(String[], String) - Method in class sc.fiji.snt.viewer.Viewer3D

Applies a custom anatomical axis mapping to the scene, setting axis labels and the scene's up vector (dorsal direction).

setAngleStepSize(double) - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

Sets the angular step size in degrees.

setAnimationAxis(Viewer3D.RotationAxis) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets the rotation axis for the live animation (double-click spin).

setAnimationEnabled(boolean) - Method in class sc.fiji.snt.viewer.MultiViewer3D

setAnimationEnabled(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Toggles the Viewer's animation.

setAnimationMode(Viewer3D.AnimationMode) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets the animation mode for both live (double-click) and recorded rotations.

setAnnotation(BrainAnnotation) - Method in class sc.fiji.snt.seed.SeedPoint

setAnnotation(BrainAnnotation) - Method in class sc.fiji.snt.util.PointInImage

setAnnotation(BrainAnnotation) - Method in interface sc.fiji.snt.util.SNTPoint

Assigns a neuropil annotation (e.g., atlas compartment) to this point.

setAnnotation(BrainAnnotation) - Method in class sc.fiji.snt.util.SWCPoint

setAnnotations(Collection<SNTPoint>, float, Color) - Method in class sc.fiji.snt.viewer.Bvv.AnnotationOverlay

Replace the current annotations with the provided list.

setAnnotationsColor(Color) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

setAnnotationsColorAllPanes(Color) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

setAnnotationsVisible(boolean) - Method in class sc.fiji.snt.SNT

Enables/Disables SNT overlays over tracing views.

setApplyCallback(Consumer<AutoTraceConfig>) - Method in class sc.fiji.snt.gui.cmds.AutoTraceConfigDialog

Sets the callback invoked when "Apply Selected" is clicked.

setAutoDetectAnimationAxis(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Enables or disables automatic detection of the best rotation axis based on the current viewpoint.

setAutoDismiss(JDialog) - Static method in class sc.fiji.snt.gui.GuiUtils

setAutoFilter(boolean) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Enables or disables automatic soma filtering in AbstractGWDTTracer.traceMultiSoma(List).

setAutoLayout(boolean) - Method in class sc.fiji.snt.gui.ComponentMover

Set the auto layout property

setAutosaveFile(File) - Method in class sc.fiji.snt.SNTPrefs

setAutoTune(boolean) - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Enables automatic parameter tuning from path and image statistics.

setAWTColor(Color) - Method in class sc.fiji.snt.util.SNTColor

Re-assigns an AWT color.

setAxesFromOmeXml(ImgPlus<?>, String) - Static method in class sc.fiji.snt.io.OmeAxisUtils

Set axes on ImgPlus from OME-XML file.

setAxesFromOmeZarrAttrs(ImgPlus<?>, String) - Static method in class sc.fiji.snt.io.OmeAxisUtils

Set axes on ImgPlus from OME-Zarr .zattrs file (level 0).

setAxesFromOmeZarrAttrs(ImgPlus<?>, String, int) - Static method in class sc.fiji.snt.io.OmeAxisUtils

Set axes on ImgPlus from OME-Zarr .zattrs file for a specific resolution level.

setAxesFromZarr(ImgPlus<?>, String) - Static method in class sc.fiji.snt.io.OmeAxisUtils

Set ImgPlus axes from OME-Zarr metadata (local or remote), level 0.

setAxesFromZarr(ImgPlus<?>, String, int) - Static method in class sc.fiji.snt.io.OmeAxisUtils

Set ImgPlus axes from OME-Zarr metadata (local or remote) at specific level.

setAxesFromZarr(ImgPlus<?>, String, int, int) - Static method in class sc.fiji.snt.io.OmeAxisUtils

Set ImgPlus axes from OME-Zarr metadata (local or remote) at specific level and series.

setAxesLabels(String...) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets custom labels for the 3D coordinate axes.

setAxesVisible(boolean) - Method in class sc.fiji.snt.analysis.SNTChart

Sets the visibility of chart axes.

setAxesVisible(boolean) - Method in class sc.fiji.snt.viewer.MultiViewer2D

setAxesVisible(boolean) - Method in class sc.fiji.snt.viewer.Viewer2D

setAxialRes(double) - Method in class sc.fiji.snt.util.TreeToRaster

Sets the axial (z) voxel size.

setBackgroundThreshold(double) - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Sets the background fraction threshold.

setBackgroundThreshold(double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the background threshold.

setBaseColor(Color) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

setBorderless() - Method in class sc.fiji.snt.gui.SNTSearchableBar

setBottomPanel(JPanel) - Method in class sc.fiji.snt.gui.OntologyBrowser.OntologyTab

Adds a bottom panel (e.g., buttons) below the tree.

setBottomPaneVisible(boolean) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

setBoundingBox(BoundingBox) - Method in class sc.fiji.snt.Tree

Associates a bounding box to this tree.

setBoundingBoxColor(String) - Method in class sc.fiji.snt.viewer.OBJMesh

Determines whether the mesh bounding box should be displayed.

setBoundingBoxColor(ColorRGB) - Method in class sc.fiji.snt.viewer.Annotation3D

Determines whether the mesh bounding box should be displayed.

setBoundingBoxColor(ColorRGB) - Method in class sc.fiji.snt.viewer.OBJMesh

Determines whether the mesh bounding box should be displayed.

setBounds(float, float, float, float, float, float) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets a manual bounding box for the scene.

setBranchFrom(Path, PointInImage) - Method in class sc.fiji.snt.Path

Establishes this path as a child path originating from the specified parent path.

setBranchTuneMaxAngle(double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the maximum angle (in degrees) for the branch tuning turn test.

setCalibration(double[], String) - Method in class sc.fiji.snt.io.SpimDataUtils.CalibratedSource

Updates the voxel calibration (spacing and unit) of this source.

setCalibration(double[], String) - Method in class sc.fiji.snt.viewer.Bvv

Overrides the voxel calibration (spacing and unit) for all loaded sources.

setCaliperFraction(double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the fraction of the nearest-neighbor soma distance used as the caliper radius for Fast Marching spread in multi-soma tracing.

setCanvasLabel(String) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Sets the string to be rendered on canvas' upper left corner.

setCanvasLabelAllPanes(String) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

setCanvasLabelBackground(Color) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Sets the background color for the canvas label.

setCanvasLabelBackgroundAllPanes(Color) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

setCanvasOffset(double, double, double) - Method in class sc.fiji.snt.viewer.Bvv

Offsets all paths being rendered.

setCanvasOffset(PointInCanvas) - Method in class sc.fiji.snt.Path

Specifies a translation offset when rendering this Path in a TracerCanvas.

setCCFVersion(String) - Static method in class sc.fiji.snt.io.MouseLightQuerier

Sets the version of the Common Coordinate Framework to be used by the Querier.

setCellColorsFromGraph() - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter

setCellRenderer(TreeCellRenderer) - Method in class sc.fiji.snt.gui.OntologyBrowser.OntologyTab

Sets a custom cell renderer for the tree.

setCenter(double[]) - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

Sets the center of the profile.

setCenter(double, double) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D

setCenter(double, double, double) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

Sets the center of analysis using real world (calibrated) coordinates.

setCenter(int) - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

Computes the center of the Profile.

setCenter(PointInImage) - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

Sets the center of the profile.

setCenter(ShollPoint) - Method in class sc.fiji.snt.analysis.sholl.Profile

setCenterFromROI() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

Computes the center of analysis from the centroid of the active ROI.

setCenterFromROI(Roi) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

Computes the center of analysis from the centroid of the specified ROI.

setCenterPx(int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D

setCenterPx(int, int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

Sets the center of analysis using image (pixel) coordinates.

setCenterSource(boolean) - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutGrouped

setChangeCursor(boolean) - Method in class sc.fiji.snt.gui.ComponentMover

Set the change cursor property

setChannelColors(Color...) - Method in class sc.fiji.snt.viewer.Bvv

Sets per-channel colors across all source groups, assigning colors sequentially by global channel order across all groups.

setChannelColors(String...) - Method in class sc.fiji.snt.viewer.Bvv

Script-friendly method for setting per-channel colors

setChannelColors(BvvMultiSource, Color...) - Method in class sc.fiji.snt.viewer.Bvv

Sets per-channel colors for a specific source group.

setChartTitle(String) - Method in class sc.fiji.snt.analysis.SNTChart

setCheckBoxEnabledPredicate(Predicate<Object>) - Method in class sc.fiji.snt.gui.OntologyBrowser.OntologyTab

Sets a predicate that controls which nodes have enabled checkboxes.

setCheckboxSelected(String, boolean) - Method in class sc.fiji.snt.gui.OntologyBrowser.OntologyTab

Programmatically checks the node whose user object's toString() matches the given label.

setChildren(Set<Path>) - Method in class sc.fiji.snt.Path

setClipAnnotationsToSlab(boolean) - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Restricts annotation/marker rendering to the slab Z range when true.

setClipPathsToSlab(boolean) - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Restricts path rendering to the slab Z range when true.

setClippingDistance(float) - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Enables or disables 'clipped visibility' for path overlays.

setClosedColor(Color) - Method in class sc.fiji.snt.tracing.artist.BiSearchArtist

Sets the color for closed nodes.

setClosedColor(Color) - Method in class sc.fiji.snt.tracing.artist.FillerThreadArtist

setClosedColor(Color) - Method in class sc.fiji.snt.tracing.artist.SearchThreadArtist

setCollapsed(boolean) - Method in class sc.fiji.snt.gui.CollapsiblePanel

Sets the collapsed state of this panel.

setColor(Color) - Method in class sc.fiji.snt.Path.PathNode

setColor(Color) - Method in class sc.fiji.snt.Path

Sets this path color.

setColor(Color) - Method in class sc.fiji.snt.util.SWCPoint

Sets the color of this point.

setColor(String) - Method in class sc.fiji.snt.Tree

Assigns a color to all the paths in this tree.

setColor(String) - Method in class sc.fiji.snt.viewer.Annotation3D

Script friendly method to assign a color to the annotation.

setColor(String, double) - Method in class sc.fiji.snt.Tree

Assigns a color to all the paths in this tree.

setColor(String, double) - Method in class sc.fiji.snt.viewer.Annotation3D

Script friendly method to assign a color to the annotation.

setColor(String, double) - Method in class sc.fiji.snt.viewer.OBJMesh

Script friendly method to assign a color to the mesh.

setColor(ARGBType) - Method in class sc.fiji.snt.viewer.BvvMultiSource

Sets the color for all sources in the group.

setColor(ColorRGB) - Method in class sc.fiji.snt.Path

Sets this path color.

setColor(ColorRGB) - Method in class sc.fiji.snt.Tree

Assigns a color to all the paths in this tree.

setColor(ColorRGB, double) - Method in class sc.fiji.snt.viewer.Annotation3D

Assigns a color to the annotation.

setColor(ColorRGB, double) - Method in class sc.fiji.snt.viewer.OBJMesh

Assigns a color to the mesh.

setColorBarLegend(String, double, double) - Method in class sc.fiji.snt.viewer.MultiViewer2D

setColorBarLegend(ColorTable, double, double, int) - Method in class sc.fiji.snt.viewer.MultiViewer2D

setColorBarLegend(T) - Method in class sc.fiji.snt.viewer.MultiViewer2D

setColorCode(boolean) - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutGrouped

setColorImage(ImagePlus) - Method in class sc.fiji.snt.SNT

Deprecated.

setColorMode(SeedOverlay.ColorMode) - Method in class sc.fiji.snt.seed.SeedOverlay

Sets the rendering color mode.

setColors(String...) - Method in class sc.fiji.snt.analysis.SNTChart

(Re)colors existing dataset series

setColors(ColorTable) - Method in class sc.fiji.snt.analysis.SNTChart

(Re)colors existing dataset series

setColorTable(String) - Method in class sc.fiji.snt.seed.SeedOverlay

Sets the active LUT.

setColorTable(ColorTable) - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutGrouped

setColorWeight(double) - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Sets the weight for the color (cosine similarity) penalty term.

setCombinedSelectionFilters(boolean) - Method in class sc.fiji.snt.PathManagerUI

Sets whether selection filters should be combined.

setConfidenceRange(double, double) - Method in class sc.fiji.snt.seed.SeedOverlay

Sets the visible confidence range.

setConnectComponents(boolean) - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Sets whether to connect nearby skeleton components.

setConnectivityType(int) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the connectivity type for Fast Marching.

setConnectivityType(int) - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

Sets the connectivity type for Fast Marching.

setConnectivityType(int) - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

Sets the connectivity type for neighbor iteration.

setConnectivityType(int) - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

Sets the connectivity type for neighbor iteration.

setContext(Context) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollTable

Sets the services required by this ShollTable, namely PrefService, used to read advanced options set by ShollAnalysisPrefsCmd.

setContext(Context) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

setContext(Context) - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

setContext(Context) - Method in class sc.fiji.snt.analysis.SNTTable

Sets a SciJava context to this table.

setContext(Context) - Static method in class sc.fiji.snt.SNTUtils

setContext(Context) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

setContext(Context) - Method in class sc.fiji.snt.viewer.GraphViewer

Sets the SciJava context for this viewer.

setConvergenceThreshold(double) - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Sets the convergence threshold for the refinement loop.

setCosSimilarityThreshold(double) - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Sets the cosine similarity threshold below which a voxel is considered spectrally dissimilar to the reference color.

setCostFunction(Cost) - Method in class sc.fiji.snt.tracing.auto.ComponentReconnector

Sets the cost function for A* searches.

setCostType(SNT.CostType) - Method in class sc.fiji.snt.SNT

setCrosshairs(double, double, double, boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Deprecated.

setCrossSectionRadius(double) - Method in class sc.fiji.snt.PathFitter

Sets the radius of cross-sectional planes sampled around each node.

setCTposition(int, int) - Method in class sc.fiji.snt.Path

Sets the hyperstack position of this Path

setCurrentDirectory(File) - Method in class sc.fiji.snt.gui.FileChooser

setCurrentFile(File) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

setCurrentPath(Path) - Method in class sc.fiji.snt.SNT

setCursorText(String) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

Sets the string to be appended to the current cursor.

setCursorTextAllPanes(String) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

setDataMode(ShollStats.DataMode) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

setDataMode(ShollStats.DataMode) - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

setDataMode(ShollStats.DataMode) - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

setDataMode(ShollStats.DataMode) - Method in interface sc.fiji.snt.analysis.sholl.math.ShollStats

setDebug(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

setDebug(boolean) - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

setDebug(boolean) - Method in class sc.fiji.snt.util.Logger

Sets the debug mode state.

setDebugMode(boolean) - Static method in class sc.fiji.snt.SNTUtils

Enables/disables debug mode

setDefaultColor(ColorRGB) - Method in class sc.fiji.snt.viewer.Viewer2D

Sets the default (fallback) color for plotting paths.

setDefaultColor(ColorRGB) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets the default color for rendering Trees.

setDefaultFontScale(double) - Static method in class sc.fiji.snt.analysis.SNTChart

setDefaultRadius(double) - Method in class sc.fiji.snt.util.TreeToRaster

Sets the default radius used for nodes/trees that have no radii defined.

setDefaultThickness(float) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets the line thickness for rendering Trees that have no specified radius.

setDefaultTransparency(int) - Method in class sc.fiji.snt.TracerCanvas

setDepthFog(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Enables or disables depth fog for all trees (current and future).

setDeselectedColor(Color) - Method in class sc.fiji.snt.SNT

setDetailedAnalysis(boolean) - Method in class sc.fiji.snt.plugin.StrahlerCmd

Whether run calls should output detailed tables and plots

setDetailedSummary(boolean) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollTable

Sets whether extensive metrics should be listed when outputting summaries.

setDigIn(boolean) - Method in class sc.fiji.snt.gui.OntologyBrowser.OntologyTab

Sets whether checking a parent automatically checks all children.

setDimensions(long, long, long) - Method in class sc.fiji.snt.util.BoundingBox

Sets the dimensions of this bounding box using uncalibrated (pixel) lengths.

setDimmedAlpha(int, int) - Method in class sc.fiji.snt.MultiPathTracerCanvas

Sets the in-band / out-of-band transparency for non-highlighted entries (percent).

setDisplayedHemisphere(String) - Method in class sc.fiji.snt.viewer.OBJMesh

Sets which hemisphere of this mesh is displayed.

setDisplayRadii(boolean) - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Controls whether paths are rendered as tapered frustums with per-node radii (true) or as simple anti-aliased lines (false).

setDisplayRadii(boolean) - Method in class sc.fiji.snt.viewer.Bvv

Sets whether paths are rendered as tapered frusta with per-node radii (true) or as anti-aliased lines (false).

setDisplayRange(double, double) - Method in class sc.fiji.snt.viewer.BvvMultiSource

Sets the display range for all sources in the group.

setDisplayRange(BvvMultiSource, double, double) - Method in class sc.fiji.snt.viewer.Bvv

Sets the display range (min/max intensity) for all channels of a specific source group.

setDistance(long, double) - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

setDistance(long, double) - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

setDistance(long, double) - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

setDistance(long, double) - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Set Fast Marching distance at linear index.

setDragInsets(Insets) - Method in class sc.fiji.snt.gui.ComponentMover

Set the drag insets.

setDrawCrosshairs(boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

setDrawCrosshairsAllPanes(boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

setDrawDiameters(boolean) - Method in class sc.fiji.snt.SNT

setDrawingThreshold(double) - Method in class sc.fiji.snt.tracing.artist.BiSearchArtist

Sets the drawing threshold for visualization.

setDrawingThreshold(double) - Method in class sc.fiji.snt.tracing.artist.SearchThreadArtist

setEdgeColor(E, ColorRGB) - Method in class sc.fiji.snt.analysis.graph.SNTGraph

setEdgeColor(E, ColorRGB) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter

setEdgeColor(E, ColorRGB) - Method in class sc.fiji.snt.viewer.geditor.SNTPseudographAdapter

setEdgeColor(AnnotationWeightedEdge, ColorRGB) - Method in class sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter

setEdgeColor(SWCWeightedEdge, ColorRGB) - Method in class sc.fiji.snt.viewer.geditor.TreeGraphAdapter

setEdgeInsets(Insets) - Method in class sc.fiji.snt.gui.ComponentMover

Set the edge insets.

setEditable(boolean) - Method in class sc.fiji.snt.PathNodeCanvas

Enables the node as editable/non-editable.

setEditableNode(int) - Method in class sc.fiji.snt.Path

Tags the specified point position as 'editable'.

setEditableNodeLocked(boolean) - Method in class sc.fiji.snt.Path

setEditingPath(Path) - Method in class sc.fiji.snt.SNT

setEitherSide(int) - Method in class sc.fiji.snt.MultiPathTracerCanvas

Sets the z-slice band (either side of the current slice) over which paths still render (with reduced alpha).

setEnableAxes(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Enables/disables the display of X,Y,Z axis grid.

setEnableCurveFitting(boolean) - Method in class sc.fiji.snt.analysis.ShollAnalyzer

Sets whether curve fitting computations should be performed.

setEnabled(boolean) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.DeepCheck

setEnabled(boolean) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.LiveCheck

setEnabled(boolean) - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

setEnabled(boolean) - Method in class sc.fiji.snt.gui.CheckboxSpinner

setEnableDarkMode(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Enables/disables "Dark Mode" mode

setEnableDebugMode(boolean) - Method in class sc.fiji.snt.SNTUI

Enables/disables debug mode

setEnableDebugMode(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Enables/disables debug mode

setEnabledNone() - Method in class sc.fiji.snt.FillManagerUI

setEnabledWhileFilling() - Method in class sc.fiji.snt.FillManagerUI

setEnabledWhileNotFilling() - Method in class sc.fiji.snt.FillManagerUI

setEnableEdgeLabels(boolean) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter

setEnableVertexLabels(boolean) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter

setEntries(List<MultiPathTracerCanvas.Entry>) - Method in class sc.fiji.snt.MultiPathTracerCanvas

Replaces the current set of painted entries with the supplied list.

setEqualizeAxes(boolean) - Method in class sc.fiji.snt.analysis.SNTChart

Sets whether the axes of the underlying XY plot should be equalized (same scale).

setEqualizeAxes(boolean) - Method in class sc.fiji.snt.viewer.Viewer2D

/** Sets whether the axes should be equalized (same scale).

setExactMetricMatch(boolean) - Static method in class sc.fiji.snt.analysis.TreeStatistics

Sets whether approximate string matching ('fuzzy matching') should be used when retrieving metrics.

setExtraMeasurement(String, String) - Method in class sc.fiji.snt.analysis.sholl.Profile

setFFromGoal(double) - Method in class sc.fiji.snt.tracing.BiSearchNode

setFFromStart(double) - Method in class sc.fiji.snt.tracing.BiSearchNode

setFileChooserTitle(String) - Method in class sc.fiji.snt.gui.FilePicker

Sets the FileChooser title

setFileFilter(FileFilter) - Method in class sc.fiji.snt.gui.FileChooser

setFileHidingEnabled(boolean) - Method in class sc.fiji.snt.gui.FileChooser

setFileUUID(UUID) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

setFillList(List<Fill>) - Method in class sc.fiji.snt.FillManagerUI

setFillList(List<Fill>) - Method in class sc.fiji.snt.PathManagerUI

setFillList(List<Fill>) - Method in class sc.fiji.snt.SNT

setFillListVisible(boolean) - Method in class sc.fiji.snt.SNTUI

setFillThreshold(double) - Method in class sc.fiji.snt.SNT

Sets the fill threshold distance.

setFillThresholdFrom(double, double, double) - Method in class sc.fiji.snt.SNT

setFillTransparent(boolean) - Method in class sc.fiji.snt.FillManagerUI

Sets the transparency state of fills.

setFillTransparent(boolean) - Method in class sc.fiji.snt.SNT

setFilterType(SNT.FilterType) - Method in class sc.fiji.snt.SNT

setFirstRunAfterUpdate(boolean) - Static method in class sc.fiji.snt.SNTPrefs

setFitted(Path) - Method in class sc.fiji.snt.Path

setFittedCircles(int, double[], double[], double[], double[], double[], double[], double[]) - Method in class sc.fiji.snt.Path

setFogIntensity(float) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets the fog intensity for all trees and persists the preference.

setFont(Font, float, ColorRGB) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets the font for label annotations

setFontSize(float) - Method in class sc.fiji.snt.analysis.SNTChart

Sets the font size to all components of this chart.

setFontSize(float, String) - Method in class sc.fiji.snt.analysis.SNTChart

Sets the font size for this chart.

setFrameSize(int, int) - Method in class sc.fiji.snt.viewer.Viewer3D

Resizes the viewer to the specified dimensions.

setFrom(double, double, BiSearchNode, boolean) - Method in class sc.fiji.snt.tracing.BiSearchNode

setFrom(DefaultSearchNode) - Method in class sc.fiji.snt.tracing.DefaultSearchNode

setFromGoal(double, double, BiSearchNode) - Method in class sc.fiji.snt.tracing.BiSearchNode

setFromStart(double, double, BiSearchNode) - Method in class sc.fiji.snt.tracing.BiSearchNode

setGap(int) - Method in class sc.fiji.snt.viewer.MultiViewer3D

setGaussianBlur(double) - Method in class sc.fiji.snt.util.TreeToRaster

Enables Gaussian blurring of the (optionally noisy) image, simulating spatially correlated noise and optical blur.

setGaussianFitVisible(boolean) - Method in class sc.fiji.snt.analysis.SNTChart

Sets whether a normal distribution curve should be overlaid over histogram frequencies.

setGFromGoal(double) - Method in class sc.fiji.snt.tracing.BiSearchNode

setGFromStart(double) - Method in class sc.fiji.snt.tracing.BiSearchNode

setGMMFitVisible(boolean) - Method in class sc.fiji.snt.analysis.SNTChart

Sets whether a GMM distribution curve should be overlaid over histogram frequencies.

setGradientShells(Color, Color) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

setGridlinesVisible(boolean) - Method in class sc.fiji.snt.analysis.SNTChart

setGridlinesVisible(boolean) - Method in class sc.fiji.snt.viewer.MultiViewer2D

setGridlinesVisible(boolean) - Method in class sc.fiji.snt.viewer.Viewer2D

setGuessedTangents(int) - Method in class sc.fiji.snt.Path

setGuiUtils(GuiUtils) - Method in class sc.fiji.snt.gui.SNTSearchableBar

setGWDT(long, double) - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

setGWDT(long, double) - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

setGWDT(long, double) - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

setGWDT(long, double) - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Overwrites the GWDT value at a linear index.

setHandle(AddressableHeap.Handle<DefaultSearchNode, Void>) - Method in class sc.fiji.snt.tracing.DefaultSearchNode

setHeadless(boolean) - Method in class sc.fiji.snt.PathAndFillManager

Sets whether this PathAndFillManager instance should run headless.

setHeapHandle(AddressableHeap.Handle<BiSearchNode, Void>, boolean) - Method in class sc.fiji.snt.tracing.BiSearchNode

setHeapHandleFromGoal(AddressableHeap.Handle<BiSearchNode, Void>) - Method in class sc.fiji.snt.tracing.BiSearchNode

setHeapHandleFromStart(AddressableHeap.Handle<BiSearchNode, Void>) - Method in class sc.fiji.snt.tracing.BiSearchNode

setHemiShells(String) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

setHemisphere(char) - Method in class sc.fiji.snt.seed.SeedPoint

setHemisphere(char) - Method in class sc.fiji.snt.util.PointInImage

setHemisphere(char) - Method in interface sc.fiji.snt.util.SNTPoint

setHemisphere(Object) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

setHeuristic(Heuristic) - Method in class sc.fiji.snt.tracing.auto.ComponentReconnector

Sets the heuristic for A* searches.

setHeuristicType(SNT.HeuristicType) - Method in class sc.fiji.snt.SNT

setHighlightedAlpha(int, int) - Method in class sc.fiji.snt.MultiPathTracerCanvas

Sets the in-band / out-of-band transparency for highlighted entries (percent).

setID(int) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

setIdentifier(String) - Method in class sc.fiji.snt.analysis.sholl.Profile

setIDs(int, int) - Method in class sc.fiji.snt.Path

setImage(RandomAccessibleInterval<? extends RealType<?>>) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.SignalQuality

Provides the image data for signal quality assessment.

setImage(RandomAccessibleInterval<? extends RealType<?>>) - Method in class sc.fiji.snt.PathFitter

Sets the target image

setImageData(RandomAccessibleInterval<? extends RealType<?>>) - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

Sets the image data used by checks that require it (e.g., PlausibilityCheck.SignalQuality).

setImageStats(double, double) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.SignalQuality

Sets image-level statistics used to auto-compute the contrast threshold when PlausibilityCheck.SignalQuality.getMinContrast() == PlausibilityCheck.SignalQuality.AUTO_THRESHOLD.

setImageStats(double, double) - Method in class sc.fiji.snt.analysis.curation.PlausibilityMonitor

Sets image-level statistics for auto-threshold computation.

setIntensityRange(double, double) - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Sets the intensity range for adaptive percent-C computation.

setIntensityWeight(double) - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Sets the weight for the intensity background penalty term.

setIntersectedVolumeAsExtraMeasurement(boolean) - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

Enables storing the intersected arbor volume as a per-shell extra measurement in the resulting Profile.

setIsIntDensityProfile(boolean) - Method in class sc.fiji.snt.analysis.sholl.Profile

setIsLoading(boolean) - Static method in class sc.fiji.snt.SNTUtils

setIsPrimary(boolean) - Method in class sc.fiji.snt.Path

setJointLeafPruneEnabled(boolean) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Enables or disables joint leaf pruning independently of leaf pruning.

setLabel(String) - Method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

Sets the optional description for the analysis

setLabel(String) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph

Sets an identifying label for this subgraph.

setLabel(String) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics

Sets an identifying label for the group of Trees being analyzed.

setLabel(String) - Method in class sc.fiji.snt.analysis.NodeStatistics

Sets a descriptive label to this statistic analysis to be used in histograms, etc.

setLabel(String) - Method in class sc.fiji.snt.gui.FilePicker

Sets the File Picker label

setLabel(String) - Method in class sc.fiji.snt.Tree

Sets an identifying label for this Tree.

setLabel(String) - Method in class sc.fiji.snt.viewer.Annotation3D

setLabel(String) - Method in class sc.fiji.snt.viewer.MultiViewer2D

Deprecated.

setLabel(String) - Method in class sc.fiji.snt.viewer.OBJMesh

Sets the label for this mesh.

setLabelLocation(float, float) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets the location for annotation labels

setLabels(List<String>) - Method in class sc.fiji.snt.viewer.MultiViewer3D

setLanguage(String) - Method in class sc.fiji.snt.gui.ScriptRecorder

Sets the recording language.

setLastKnownDir(File) - Static method in class sc.fiji.snt.SNTPrefs

setLateralRes(double) - Method in class sc.fiji.snt.util.TreeToRaster

Sets the lateral (x, y) voxel size.

setLayoutColumns(int) - Method in class sc.fiji.snt.viewer.MultiViewer2D

setLayoutColumns(int) - Method in class sc.fiji.snt.viewer.MultiViewer3D

setLeafPruneOverlap(double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the leaf pruning overlap threshold.

setLegend(String, double, double) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

setLegend(String, String, double, double) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

setLegend(ColorTable, String, double, double) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

setLegend(GraphEditor) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

setLegendVisible(boolean) - Method in class sc.fiji.snt.analysis.SNTChart

setLengthThreshold(double) - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Sets the minimum component length necessary to avoid pruning.

setLineWidth(int) - Method in class sc.fiji.snt.analysis.SNTChart

Changes the line width of all series in a XY plot

setLiveSync(boolean) - Method in class sc.fiji.snt.viewer.BvvMultiSource

Sets whether transforms are propagated to followers on every render frame (true) or only on explicit BvvMultiSource.syncTransforms() calls (false).

setLockCursor(boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

setLockCursorAllPanes(boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

setLogger(Logger) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

setLogger(Logger) - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

setLogger(Logger, boolean) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

setLogger(Logger, boolean) - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

setLookAndFeel() - Static method in class sc.fiji.snt.gui.GuiUtils

setLookAndFeel(String) - Static method in class sc.fiji.snt.SNTPrefs

Sets the look and feel preference.

setLookAndFeel(String) - Method in class sc.fiji.snt.SNTUI

setLookAndFeel(String) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

setLookAndFeel(String) - Method in class sc.fiji.snt.viewer.Viewer3D

setLookAndFeel(String, boolean) - Static method in class sc.fiji.snt.gui.GuiUtils

setLookAndFeel(String, boolean, Component...) - Static method in class sc.fiji.snt.gui.GuiUtils

setLowerPercentile(double) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCalibrator

Sets the percentile used for "flag if below" thresholds (e.g., min fork angle, min terminal branch length).

setLut(ImagePlus, String) - Static method in class sc.fiji.snt.util.ImpUtils

setMaxAngleDeg(double) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.BranchAngle

setMaxAngleDeg(double) - Method in class sc.fiji.snt.tracing.auto.ComponentReconnector

Sets the maximum angle (in degrees) between the bridge tangent and the existing branch direction at connection points.

setMaxBridgeDistVoxels(double) - Method in class sc.fiji.snt.tracing.auto.ComponentReconnector

Sets the maximum Euclidean distance (in voxels) between candidate endpoints.

setMaxConnectDist(double) - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Sets the maximum distance for connecting skeleton components.

setMaxContractionDiff(double) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.TortuosityConsistency

setMaxDistUm(double) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.SomaDistance

setMaxEvaluations(int) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Sets the function evaluation limit for solvers.

setMaxGapVoxels(int) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the maximum number of consecutive dark voxels that Fast Marching can bridge during tracing.

setMaxIterations(int) - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Sets the maximum number of iterations for the refinement loop.

setMaxJumpRatio(double) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.RadiusJumps

setMaxOrder(int) - Method in class sc.fiji.snt.plugin.ij1.Strahler

Sets the maximum Strahler order to be considered by the plugin.

setMaxRadius(int) - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Sets the maximum radius (in pixels) to test during radius optimization.

setMaxRatio(double) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.RadiusContinuity

setMaxThickness(float) - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Sets the maximum thickness for path rendering.

setMeshBackfaceCull(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Enables or disables backface culling for all OBJ meshes (current and future).

setMeshShadingMode(int) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets the shading mode for all OBJ meshes (current and future).

setMetric(ProfileProcessor.Metric) - Method in class sc.fiji.snt.analysis.PathProfiler

setMetric(ProfileProcessor.Metric) - Method in class sc.fiji.snt.analysis.ProfileProcessor

Sets the metric to be computed for each local neighborhood.

setMetric(SNT.CostType) - Method in class sc.fiji.snt.Fill

Sets the cost metric for the filled structure.

setMinAlignmentDeg(double) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.DirectionContinuity

setMinAngleDeg(double) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.BranchAngle

setMinBranchIntensityLength(double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the minimum branch intensity-length threshold.

setMinContraction(double) - Method in class sc.fiji.snt.tracing.auto.ComponentReconnector

Sets the minimum contraction (Euclidean distance / path length) for accepting a bridge.

setMinContrast(double) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.SignalQuality

Sets the minimum signal-to-background contrast ratio below which a path is flagged.

setMinIncreasingRun(int) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.RadiusMonotonicity

setMinLengthUm(double) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.TerminalBranchLength

setMinMax(double, double) - Method in class sc.fiji.snt.analysis.ColorMapper

Sets the LUT mapping bounds.

setMinMax(double, double) - Method in class sc.fiji.snt.analysis.graph.GraphColorMapper

setMinMax(double, double) - Method in class sc.fiji.snt.analysis.NodeColorMapper

setMinMeanIntensity(double) - Method in class sc.fiji.snt.tracing.auto.ComponentReconnector

Sets the minimum mean intensity along the bridge path.

setMinNBins(int) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Sets the minimum number of bins when assembling histograms.

setMinPathLength(double) - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Sets the minimum path length for analysis inclusion.

setMinSegmentLength(double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Deprecated.

Use AbstractGWDTTracer.setMinBranchIntensityLength(double) instead. Note: the physical-to-voxel conversion is not meaningful for this parameter since it is an intensity sum, not a distance.

setMinSegmentLengthVoxels(double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Deprecated.

Use AbstractGWDTTracer.setMinBranchIntensityLength(double) instead.

setMinSomaDistance(double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the minimum distance (in voxels) between soma centers for multi-soma tracing.

setMinThickness(float) - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Sets the minimum thickness for path rendering.

setMinTimePoints(int) - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Sets the minimum number of time points required for analysis.

setModified(boolean) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

setName(String) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

setName(String) - Method in class sc.fiji.snt.Path

Sets this Path's name.

setNaNColor(Color) - Method in class sc.fiji.snt.analysis.ColorMapper

Sets the color to use for NaN (Not a Number) values.

setNDimensions(int) - Method in class sc.fiji.snt.analysis.sholl.Profile

setNextImgExtensions(String) - Method in class sc.fiji.snt.SNTPrefs

Convenience method for setting filename suffixes from a comma-separated string.

setNextImgExtensions(List<String>) - Method in class sc.fiji.snt.SNTPrefs

Sets the list of filename suffixes used to identify images when navigating to the next/previous image in a folder.

setNodeAnnotation(BrainAnnotation, int) - Method in class sc.fiji.snt.Path

Assigns an annotation to an existing node.

setNodeColor(Color, int) - Method in class sc.fiji.snt.Path

Sets the node color.

setNodeColor(ColorRGB, int) - Method in class sc.fiji.snt.Path

Sets the node color.

setNodeColors(Color[]) - Method in class sc.fiji.snt.Path

Sets the node colors.

setNodeDiameter(double) - Method in class sc.fiji.snt.TracerCanvas

Sets the baseline for rendering diameter of path nodes

setNodeHemisphere(char, int) - Method in class sc.fiji.snt.Path

Assigns a hemisphere to an existing node.

setNodeIndicesAsDistances(boolean) - Method in class sc.fiji.snt.analysis.PathProfiler

Sets whether the profile abscissae should be reported in real-word units (the default) or node indices (zero-based).

setNodeRadius(double, int) - Method in class sc.fiji.snt.Path

Sets the radius of a specific node.

setNodeRadiusFallback(int) - Method in class sc.fiji.snt.PathFitter

Sets the fallback strategy for node radii at locations where fitting failed.

setNodeStep(int) - Method in class sc.fiji.snt.analysis.NodeProfiler

setNodeTangent(double[], int) - Method in class sc.fiji.snt.Path

Sets the tangent vector of a specific node.

setNodeTangent(double, double, double, int) - Method in class sc.fiji.snt.Path

Sets the tangent vector of a specific node.

setNodeValue(double, int) - Method in class sc.fiji.snt.Path

Assigns the "value" property to this node.

setNodeValues(double[]) - Method in class sc.fiji.snt.Path

Sets the path "values", the array containing the numeric property assigned to path nodes, typically voxel intensities.

setNSomas(int) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the expected number of somas in the image for multi-soma tracing.

setObjColor(String) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

setObjPath(String) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

setOpacity(double) - Method in class sc.fiji.snt.tracing.artist.FillerThreadArtist

setOpenColor(Color) - Method in class sc.fiji.snt.tracing.artist.BiSearchArtist

Sets the color for open nodes.

setOpenColor(Color) - Method in class sc.fiji.snt.tracing.artist.FillerThreadArtist

setOpenColor(Color) - Method in class sc.fiji.snt.tracing.artist.SearchThreadArtist

setOrder(int) - Method in class sc.fiji.snt.Path

setOrigin(PointInImage) - Method in class sc.fiji.snt.util.BoundingBox

Sets the origin for this box, i.e., its (xMin, yMin, zMin) vertex.

setOriginOpposite(PointInImage) - Method in class sc.fiji.snt.util.BoundingBox

Sets the origin opposite for this box, i.e., its (xMax, yMax, zMax) vertex.

setOrigIP(ImagePlus) - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Sets the original ImagePlus to be used during voxel-based loop pruning.

setOutlineVisible(boolean) - Method in class sc.fiji.snt.analysis.SNTChart

Sets the visibility of the plot outline.

setOutlineVisible(boolean) - Method in class sc.fiji.snt.viewer.MultiViewer2D

setOutlineVisible(boolean) - Method in class sc.fiji.snt.viewer.Viewer2D

setOutOfBoundsTransparency(int) - Method in class sc.fiji.snt.TracerCanvas

setOvershootRemovalEnabled(boolean) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Enables or disables overshoot removal.

setParallelBranchPruneEnabled(boolean) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Enables or disables parallel branch pruning.

setParent(long, long) - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

setParent(long, long) - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

setParent(long, long) - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

setParent(long, long) - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Set parent pointer at linear index.

setParent(Component) - Method in class sc.fiji.snt.gui.GuiUtils

setParent(Window) - Method in class sc.fiji.snt.gui.CostPalette

setParent(Window) - Method in class sc.fiji.snt.gui.SigmaPalette

setParent(BrainAnnotation) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

setParentToActiveWindow() - Method in class sc.fiji.snt.gui.GuiUtils

setPath(Path) - Method in class sc.fiji.snt.util.PointInImage

Associates a Path with this node

setPathFittingEnabled(boolean) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Enables or disables post-hoc path fitting using PathFitter.

setPathFormatter(Function<TreePath, String>) - Method in class sc.fiji.snt.gui.OntologyBrowser

Sets a custom formatter for converting checked TreePaths into strings.

setPathList(List<Path>, Path, boolean) - Method in class sc.fiji.snt.FillManagerUI

setPathList(List<Path>, Path, boolean) - Method in class sc.fiji.snt.PathManagerUI

setPathList(List<Path>, Path, boolean) - Method in class sc.fiji.snt.SNT

setPaths3DDisplay(int) - Method in class sc.fiji.snt.SNT

Deprecated.

setPathUnfinished(boolean) - Method in class sc.fiji.snt.SNT

setPaused(boolean) - Method in class sc.fiji.snt.gui.ScriptRecorder

Sets the pause state of the recorder.

setPercentage(int) - Method in class sc.fiji.snt.gui.GuiUtils.JTables.VisitingZoom

Sets the percentage, clamped to the allowed range.

setPercentCRange(double, double) - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Sets the percent-C range for adaptive intensity tolerance.

setPhaseSensitivity(double) - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Sets the phase detection sensitivity.

setPlateauThreshold(double) - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Sets the base threshold fraction for phase classification.

setPlugin(SNT) - Static method in class sc.fiji.snt.SNTUtils

setPointsColor(Color) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

setPointsLUT(String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

setPointsLUT(String, String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

setPointsLUT(ColorTable, String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

setPointsOpacity(double) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

setPointsSize(String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

setPoissonNoise(double, double) - Method in class sc.fiji.snt.util.TreeToRaster

Enables Poisson shot noise on the rasterized image, simulating photon counting noise typical of fluorescence microscopy.

setPolynomialFitRange(int, int) - Method in class sc.fiji.snt.analysis.ShollAnalyzer

Sets the polynomial fit range for linear Sholl statistics.

setPopupMenu(JPopupMenu) - Method in class sc.fiji.snt.gui.OntologyBrowser.OntologyTab

Sets a popup menu on the tree.

setPos(long, long) - Method in class sc.fiji.snt.util.CircleCursor3D

setPosition(int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

setPosition(int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser3D

setPosition(int, int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D

setPosition(int, int, int) - Method in class sc.fiji.snt.tracing.BiSearchNode

setPredecessor(DefaultSearchNode) - Method in class sc.fiji.snt.tracing.DefaultSearchNode

setPredecessorFromGoal(BiSearchNode) - Method in class sc.fiji.snt.tracing.BiSearchNode

setPredecessorFromStart(BiSearchNode) - Method in class sc.fiji.snt.tracing.BiSearchNode

setPreferredSize(int, int) - Method in class sc.fiji.snt.viewer.Viewer2D

Sets the preferred size of the plot to a constant value.

setPrevious(SWCPoint) - Method in class sc.fiji.snt.util.SWCPoint

Sets the preceding node in the reconstruction

setPrimaryBranches(int) - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Sets the number of primary branches associated with this profile, used to calculate ramification indices.

setProfile(Profile) - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCommonCmd

setProgressCallback(int, MultiTaskProgress) - Method in class sc.fiji.snt.PathFitter

setProperties(Properties) - Method in class sc.fiji.snt.analysis.sholl.Profile

setProximityUm(double) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCheck.PathOverlap

setPruneByLength(boolean) - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Sets whether to prune components below a threshold length from the result.

setPruneEnds(boolean) - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Sets whether to prune end branches during skeleton analysis.

setPruneMode(int) - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Sets the loop pruning strategy.

setPruneMode(BinaryTracer) - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

Configures the prune mode on a BinaryTracer based on the current BinaryTracerCommonCmd.loopSolvingChoice selection.

setPseudoLighting(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Enables or disables pseudo-lighting for all trees (current and future).

setQuartilesVisible(boolean) - Method in class sc.fiji.snt.analysis.SNTChart

Sets whether quartile markers (Q1, Median, Q3) should be overlaid over histogram frequencies.

setRadii(double) - Method in class sc.fiji.snt.Tree

Assigns a fixed radius to all the nodes in this tree.

setRadii(double[]) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

setRadii(double[]) - Method in class sc.fiji.snt.Path

Assigns radii to this Path

setRadii(double, double, double) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

setRadii(double, double, double) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D

setRadii(double, double, double, int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D

setRadiiSpan(int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser2D

setRadius(double) - Method in class sc.fiji.snt.Path.PathNode

setRadius(double) - Method in class sc.fiji.snt.Path

Assigns a fixed radius to all the nodes of this Path

setRadius(double, int) - Method in class sc.fiji.snt.Path

Assigns a radius to a specific node of this Path.

setRadius(int) - Method in class sc.fiji.snt.analysis.NodeProfiler

setRadius(int) - Method in class sc.fiji.snt.analysis.PathProfiler

setRadius(int) - Method in class sc.fiji.snt.analysis.ProfileProcessor

Specify a fixed radius for each ProfileProcessor.Shape region around each PointInImage.

setRadiusScale(float) - Method in class sc.fiji.snt.viewer.Viewer3D

Applies a scaling factor to Trees rendered as Viewer3D.ArborVBO.

setRadiusScale(Collection<String>, float) - Method in class sc.fiji.snt.viewer.Viewer3D

Applies a tube radius scale to a subset of rendered trees.

setRadiusWeight(double) - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Sets the weight for the radius expansion penalty term.

setRapidThreshold(double) - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Sets the rapid threshold multiple for phase classification.

setRecentDir(File) - Method in class sc.fiji.snt.SNTPrefs

setReconstructionViewer(Viewer3D) - Method in class sc.fiji.snt.SNTUI

setRecorder(ScriptRecorder) - Method in class sc.fiji.snt.gui.SNTCommandFinder

Sets the script recorder for this command finder.

setRecordingCall(AbstractButton, String) - Static method in class sc.fiji.snt.gui.ScriptRecorder

setReductionFactor(double) - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutScaled

setReferenceBounds(int, int, int) - Method in class sc.fiji.snt.util.TreeToRaster

Sets reference bounds explicitly, so the output image matches the specified dimensions.

setReferenceBounds(ImagePlus) - Method in class sc.fiji.snt.util.TreeToRaster

Sets reference bounds from an ImagePlus, so the output image matches its exact dimensions.

setReferenceWindowRadius(int) - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Sets the sliding-window radius for per-node reference color computation.

setRenderingHints(Graphics2D) - Static method in class sc.fiji.snt.gui.GuiUtils

setRenderingScale(double) - Method in class sc.fiji.snt.SNTUI

Sets rendering scale of Paths as per respective widget in dialog.

setReplaceNodes(boolean) - Method in class sc.fiji.snt.PathFitter

Sets whether fitting should occur "in place".

setResampleStep(double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the resampling step size in voxels.

setRetractionThreshold(double) - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Sets the retraction threshold as a fraction of length

setRetrieveIntDensities(boolean) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

setRoot(SWCPoint) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Sets the root of the tree.

setRoot(SWCPoint) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph

Sets the root of the tree.

setRootRoi(Roi, int) - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Sets the Roi enclosing the nodes to be set as root(s) in the final graphs.

setRoots(Collection<SeedPoint>) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the run's root from a collection of seeds.

setRoots(Collection<SeedPoint>) - Method in interface sc.fiji.snt.tracing.auto.AutoTracer

Hands the tracer a collection of seeds to use as roots in this run.

setRoots(Collection<SeedPoint>) - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Sets the run's root from a collection of seeds. v1 takes the first seed and bridges to the existing BinaryTracer.setRootRoi(Roi, int) API by synthesizing an oval ROI around the seed (diameter derived from SeedPoint.radius, with a minimum of one voxel when radius is unset) and using AutoTracer.ROI_CENTROID placement.

setRootVisible(boolean) - Method in class sc.fiji.snt.gui.OntologyBrowser.OntologyTab

Sets whether the root node is visible.

setSaveCompressedTraces(boolean) - Method in class sc.fiji.snt.SNTPrefs

Sets whether to save traces in compressed format.

setSaveWinLocations(boolean) - Method in class sc.fiji.snt.SNTPrefs

Sets whether window locations should be saved and restored.

setSceneUpdatesEnabled(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets whether the scene should update (refresh) every time a new reconstruction (or mesh) is added/removed from the scene.

setSciView(SciView) - Method in class sc.fiji.snt.SciViewSNT

Sets the SciView to be used.

setSciViewSNT(SciViewSNT) - Method in class sc.fiji.snt.SNTUI

setScope(int) - Method in class sc.fiji.snt.PathFitter

Sets the fitting scope.

setScoreMap(RandomAccessibleInterval<? extends RealType<?>>) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets an external score/probability map to use for per-node scoring.

setScoreMapEnabled(boolean) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Enables or disables per-node score computation using a vesselness or probability map.

setScoreMapFilterType(SNT.FilterType) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the filter type used to compute the score map internally when no external map is provided.

setScoreMapPruneThreshold(double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the minimum score threshold for score-aware pruning.

setScoreMapScales(double[]) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the scales (in physical units) for the internal vesselness filter.

setSearchableObjectDescription(String) - Method in class sc.fiji.snt.gui.SNTSearchableBar

setSearchImageType(SNT.SearchImageType) - Method in class sc.fiji.snt.SNT

setSearchType(SNT.SearchType) - Method in class sc.fiji.snt.SNT

setSecondaryImage(File) - Method in class sc.fiji.snt.SNT

Specifies the 'secondary image' to be used during a tracing session.

setSecondaryImageMinMax(double, double) - Method in class sc.fiji.snt.SNT

setSecondaryLayerTracingSelected(boolean) - Method in class sc.fiji.snt.SNTUI

setSeed(long[]) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the seed point (soma location) in voxel coordinates.

setSeedPhysical(double[]) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the seed point in physical coordinates.

setSelected(boolean) - Method in class sc.fiji.snt.gui.CheckboxSpinner

setSelected(boolean) - Method in class sc.fiji.snt.Path

setSelected(Collection<Path>, Object) - Method in class sc.fiji.snt.PathAndFillManager

setSelectedColor(Color) - Method in class sc.fiji.snt.SNT

setSelectedColor(Color, boolean) - Method in class sc.fiji.snt.gui.ColorChooserButton

setSelectedPaths(Collection<Path>, Object) - Method in class sc.fiji.snt.FillManagerUI

setSelectedPaths(Collection<Path>, Object) - Method in class sc.fiji.snt.PathManagerUI

setSelectedPaths(Collection<Path>, Object) - Method in class sc.fiji.snt.SNT

setSelectedSeeds(Collection<? extends SeedPoint>) - Method in class sc.fiji.snt.seed.SeedOverlay

Replaces the selection set.

setSex(String) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

setShape(ProfileProcessor.Shape) - Method in class sc.fiji.snt.analysis.NodeProfiler

Sets the shape of the iterating cursor.

setShape(ProfileProcessor.Shape) - Method in class sc.fiji.snt.analysis.PathProfiler

setShape(ProfileProcessor.Shape) - Method in class sc.fiji.snt.analysis.ProfileProcessor

Sets the shape to be iterated.

setShellsColor(Color) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

setShellsLUT(String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

setShellsLUT(String, String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

setShellsLUT(ColorTable, String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

setShellsOpacity(double) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

setShellsThickness(int) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

setShortestPath(boolean) - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Sets whether to calculate the longest shortest-path in the skeleton result.

setShowAnnotatedView(boolean) - Method in class sc.fiji.snt.PathFitter

Sets whether an interactive image of the result should be displayed.

setShowDirectionArrows(boolean) - Static method in class sc.fiji.snt.PathNodeCanvas

Sets whether direction arrows should be displayed on paths.

setShowOnlyActiveCTposPaths(boolean, boolean) - Method in class sc.fiji.snt.SNT

setShowOnlySelectedPaths(boolean) - Method in class sc.fiji.snt.SNT

setShowOnlySelectedPaths(boolean, boolean) - Method in class sc.fiji.snt.SNT

setSigmaPaletteListener(SigmaPaletteListener) - Method in class sc.fiji.snt.SNTUI

setSigmas(List<Double>) - Method in class sc.fiji.snt.gui.cmds.ComputeSecondaryImg

setSigmas(List<Double>) - Method in interface sc.fiji.snt.gui.SigmaPaletteListener

setSilent(boolean) - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Sets whether to run skeleton analysis in silent mode.

setSinglePane(boolean) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

setSize(double) - Method in class sc.fiji.snt.PathNodeCanvas

setSize(Number) - Method in class sc.fiji.snt.viewer.Annotation3D

Sets the annotation width.

setSkipSingleVoxels(boolean) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser3D

setSkipSomaticSegments(boolean) - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

If primary paths start far-away from the soma (expected to be defined by a single-point (soma centroid)), should segments between the soma and neurite be ignored.

setSlabZBounds(double, double) - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Sets the world-Z bounds of the current slab.

setSmoothWindowSize(int) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the smoothing window size (must be odd and ≥ 3).

setSnapshotDir(String) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets the directory for storing snapshots.

setSnapSize(Dimension) - Method in class sc.fiji.snt.gui.ComponentMover

Set the snap size.

setSomaDisplayTriangle(boolean) - Method in class sc.fiji.snt.SNTPrefs

Sets whether single-node paths tagged as soma should render w/ triangular shape.

setSomaRadius(float) - Method in class sc.fiji.snt.viewer.Viewer3D

Applies a constant radius to all rendered somas being rendered as spheres.

setSomaRadius(Collection<String>, float) - Method in class sc.fiji.snt.viewer.Viewer3D

Applies a constant radius to the somas of a subset of rendered trees.

setSomaRenderMode(int) - Static method in class sc.fiji.snt.PathNodeCanvas

Sets the rendering mode for soma nodes (single-point paths).

setSomaRoi(Roi) - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Sets the soma ROI using the default strategy (ROI_CENTROID).

setSomaRoi(Roi, int) - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Sets the soma ROI and rooting strategy.

setSomaRoiZPosition(int) - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Overrides the Z-position used to constrain the soma ROI.

setSomasDisplayed(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Toggles the visibility of somas for all trees in the scene.

setSomasDisplayed(Collection<String>, boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Toggles the visibility of somas for subset of trees.

setSortMidLevel(boolean) - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutGrouped

setSourceAnnotation(BrainAnnotation) - Method in class sc.fiji.snt.viewer.OBJMesh

Associates this mesh with the BrainAnnotation (atlas compartment) it was retrieved from.

setSourcePaths(Collection<Path>) - Method in class sc.fiji.snt.tracing.FillerThread

setSourcePaths(Set<Path>) - Method in class sc.fiji.snt.Fill

Sets the source paths for the filled structure using a set of paths.

setSourcePaths(Path[]) - Method in class sc.fiji.snt.Fill

Sets the source paths for the filled structure using an array of paths.

setSpacing(double, double, double, String) - Method in class sc.fiji.snt.Fill

setSpacing(double, double, double, String) - Method in class sc.fiji.snt.Path

setSpacing(double, double, double, String) - Method in class sc.fiji.snt.util.BoundingBox

Sets the voxel spacing.

setSpacing(Calibration) - Method in class sc.fiji.snt.Path

setSpatialCalibration(Calibration) - Method in class sc.fiji.snt.analysis.sholl.Profile

setSpeciesID(int) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

setSphereOverlapThreshold(double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the sphere overlap threshold for detecting redundant nodes during hierarchical pruning.

setSpineOrVaricosityCount(int) - Method in class sc.fiji.snt.Path

Sets the number of spines or varicosities associated with this path.

setSpinnerMinMax(int, int) - Method in class sc.fiji.snt.gui.CheckboxSpinner

setSplitDendritesFromAxons(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets whether axons and dendrites should be imported as separated objects.

setSplitFills(boolean) - Method in class sc.fiji.snt.FillManagerUI

Sets whether each path should be filled independently.

setSrRatio(double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the SR (Signal-to-Redundant) ratio threshold used in hierarchical pruning.

setStartJoin(Path, PointInImage) - Method in class sc.fiji.snt.Path

Deprecated.

use Path.setBranchFrom(Path, PointInImage) instead

setState(long, byte) - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

setState(long, byte) - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

setState(long, byte) - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

setState(long, byte) - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Set Fast Marching state at linear index.

setState(BiSearchNode.State, boolean) - Method in class sc.fiji.snt.tracing.BiSearchNode

setStateFromGoal(BiSearchNode.State) - Method in class sc.fiji.snt.tracing.BiSearchNode

setStateFromStart(BiSearchNode.State) - Method in class sc.fiji.snt.tracing.BiSearchNode

setStatus(String) - Method in class sc.fiji.snt.gui.SNTSearchableBar

setStatusLabelPlaceholder(String) - Method in class sc.fiji.snt.gui.OntologyBrowser.OntologyTab

Sets the status label placeholder text on the search bar.

setStatusLabelPlaceholder(String) - Method in class sc.fiji.snt.gui.SNTSearchableBar

setStatusListener(Consumer<String>) - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Sets a listener that receives short status messages at each major phase of the tracing pipeline (e.g.

setStepSize(double) - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

Sets the radius step size.

setStopAtThreshold(boolean) - Method in class sc.fiji.snt.tracing.FillerThread

Whether to terminate the fill operation once all nodes less than or equal to the distance threshold have been explored.

setStopFillAtThreshold(boolean) - Method in class sc.fiji.snt.SNT

setStoreExtraFillNodes(boolean) - Method in class sc.fiji.snt.SNT

setStoreExtraNodes(boolean) - Method in class sc.fiji.snt.tracing.FillerThread

Whether to store above-threshold nodes in the Fill object.

setStrokeWidth(int) - Method in class sc.fiji.snt.analysis.RoiConverter

Sets the line width of converted segment paths.

setSubFilteringEnabled(boolean) - Method in class sc.fiji.snt.gui.SNTSearchableBar

setSWCType(int) - Method in class sc.fiji.snt.Path

Sets the SWC type.

setSWCType(int) - Method in class sc.fiji.snt.util.SNTColor

Re-assigns a SWC type integer flag

setSWCType(int, boolean) - Method in class sc.fiji.snt.Path

setSWCType(String) - Method in class sc.fiji.snt.Tree

Assigns an SWC type label to all the Paths in this Tree.

setSymmetryAxis(int) - Method in class sc.fiji.snt.viewer.OBJMesh

Sets the axis defining the symmetry plane of this mesh (e.g., the sagittal plane for most bilateria models), where X=0; Y=1; Z=2;

setSyntaxStyle(String) - Method in class sc.fiji.snt.gui.SNTEditorPane

Set the language of this SNTEditorPane.

setTable(GenericTable) - Method in class sc.fiji.snt.analysis.TreeStatistics

Sets the table for this TreeStatistics instance.

setTable(GenericTable, String) - Method in class sc.fiji.snt.analysis.TreeStatistics

Sets the measurements table.

setTable(SNTTable) - Method in class sc.fiji.snt.gui.MeasureUI

setTags(String) - Method in class sc.fiji.snt.util.SWCPoint

Sets the tags associated with this point.

setTangent(double[]) - Method in class sc.fiji.snt.Path.PathNode

setTangent(double, double, double) - Method in class sc.fiji.snt.Path.PathNode

setTemp(String, boolean) - Method in class sc.fiji.snt.SNTPrefs

Sets a temporary boolean preference value that will be cleared at session end.

setTemp(String, String) - Method in class sc.fiji.snt.SNTPrefs

Sets a temporary string preference value that will be cleared at session end.

setTemporaryPath(Path) - Method in class sc.fiji.snt.SNT

setThicknessModulation(double) - Method in class sc.fiji.snt.util.TreeToRaster

Enables intensity modulation based on local neurite thickness.

setThicknessMultiplier(float) - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Sets the thickness multiplier for path rendering.

setThreads(int) - Static method in class sc.fiji.snt.SNTPrefs

Sets the number of threads to use for multi-threaded operations.

setThreshold(double) - Method in class sc.fiji.snt.Fill

Sets the distance threshold for the filled structure.

setThreshold(double) - Method in class sc.fiji.snt.tracing.FillerThread

setThreshold(double, double) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

Sets the threshold range for pixel inclusion in the analysis.

setTimeoutPerSearch(int) - Method in class sc.fiji.snt.tracing.auto.ComponentReconnector

Sets the A* search timeout per candidate pair, in seconds.

setTipExtensionDistance(double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the maximum distance (in voxels) for A*-based tip extension.

setTips(Collection<SeedPoint>) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Configures the run's tips.

setTips(Collection<SeedPoint>) - Method in interface sc.fiji.snt.tracing.auto.AutoTracer

Hands the tracer a collection of seeds to use as tips / targets in this run.

setTitle(String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollTable

setTitle(String) - Method in class sc.fiji.snt.analysis.SNTChart

setTitle(String) - Method in class sc.fiji.snt.analysis.SNTTable

Sets the title of the table.

setTitle(String) - Method in class sc.fiji.snt.viewer.MultiViewer2D

Sets the title of this Viewer's frame.

setTitle(String) - Method in class sc.fiji.snt.viewer.MultiViewer3D

Sets the title of the Viewer's frame.

setTitle(String) - Method in class sc.fiji.snt.viewer.Viewer2D

Sets the plot display title.

setTitle(String) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets the title of the Viewer's frame.

setTooltipText(String) - Method in class sc.fiji.snt.gui.CollapsiblePanel

setToolTipText(String) - Method in class sc.fiji.snt.gui.CheckboxSpinner

setTracedRegionBuffer(int) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the buffer (in voxels) applied around traced regions between passes in AbstractGWDTTracer.traceMultiSoma(List).

setTrackAliveIndices(boolean) - Method in class sc.fiji.snt.tracing.auto.gwdt.ArrayStorageBackend

setTrackAliveIndices(boolean) - Method in class sc.fiji.snt.tracing.auto.gwdt.DiskBackedStorageBackend

setTrackAliveIndices(boolean) - Method in class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

setTrackAliveIndices(boolean) - Method in interface sc.fiji.snt.tracing.auto.gwdt.StorageBackend

Enable or disable tracking of ALIVE indices during Fast Marching.

setTransparency(double) - Method in class sc.fiji.snt.analysis.AnnotationMapper

Sets the transparency level for mapped annotations.

setTransparency(double) - Method in class sc.fiji.snt.seed.SeedOverlay

Sets the global transparency multiplier (clamped to [0, 1]).

setTransparency(double) - Method in class sc.fiji.snt.viewer.Annotation3D

Script friendly method to assign a transparency to the annotation.

setTransparency(double) - Method in class sc.fiji.snt.viewer.OBJMesh

Changes the transparency of this mesh.

setTransparency(float) - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Sets the transparency level for path rendering.

setTreeColor(Collection<String>, String, String) - Method in class sc.fiji.snt.viewer.Viewer3D

Recolors a subset of rendered trees.

setTreeColor(Collection<String>, ColorRGB, String) - Method in class sc.fiji.snt.viewer.Viewer3D

Recolors a subset of rendered trees.

setTreeLabel(String) - Method in class sc.fiji.snt.Path

setTreeThickness(float) - Method in class sc.fiji.snt.viewer.Viewer3D

Applies a constant thickness to all rendered trees.

setTreeThickness(float, String) - Method in class sc.fiji.snt.viewer.Viewer3D

Applies a constant thickness (line width) to all rendered trees.Note that by default, trees are rendered using their nodes' diameter.

setTreeThickness(Collection<String>, float, String) - Method in class sc.fiji.snt.viewer.Viewer3D

Applies a constant thickness (line width) to a subset of rendered trees.

setTubeMode(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Enables or disables tube rendering for all trees (current and future).

setTubeSides(int) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets the number of sides for tube cross-sections for all trees.

setTubeWireframe(boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Enables or disables the wireframe overlay on tube rendering for all trees.

setType(int) - Method in class sc.fiji.snt.PathNodeCanvas

setType(int) - Method in class sc.fiji.snt.Tree

Assigns an SWC type label to all the Paths in this Tree.

setType(String) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

setUnit(String) - Method in class sc.fiji.snt.util.BoundingBox

Sets the default length unit for voxel spacing (typically um, for SWC reconstructions)

setUnsavedChanges(boolean) - Method in class sc.fiji.snt.SNT

setup(String, ImagePlus) - Method in class sc.fiji.snt.plugin.ij1.SummarizeSkeleton

setUpperPercentile(double) - Method in class sc.fiji.snt.analysis.curation.PlausibilityCalibrator

Sets the percentile used for "flag if above" thresholds (e.g., max fork angle, max radius ratio).

setUpsamplingFactor(int) - Method in class sc.fiji.snt.viewer.Viewer3D

Sets the Catmull-Rom upsampling factor for all trees and rebuilds them. 1 = no smoothing, higher = smoother paths at vertex joints.

setUseAbsoluteWindowSize(boolean) - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Sets whether to use absolute window size instead of fractional window size.

setUseFitted(boolean) - Method in class sc.fiji.snt.Path

Sets whether the fitted flavor of this Path should be used.

setUseGlobalThresholds(boolean) - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Sets whether to use global thresholds for phase classification.

setUsePathRadius(boolean) - Method in class sc.fiji.snt.viewer.Bvv.PathRenderingOptions

Sets whether to use path radius for thickness calculation.

setUseSubVolumeStats(boolean) - Method in class sc.fiji.snt.SNT

setUUID(UUID) - Method in class sc.fiji.snt.annotation.InsectBrainCompartment

setValue(int, int, V) - Method in class sc.fiji.snt.tracing.image.ArraySearchImage

setValue(int, int, V) - Method in class sc.fiji.snt.tracing.image.ListSearchImage

setValue(int, int, V) - Method in class sc.fiji.snt.tracing.image.MapSearchImage

setValue(int, int, V) - Method in interface sc.fiji.snt.tracing.image.SearchImage

setVerbose(boolean) - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Sets verbose logging mode.

setVerbose(boolean) - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

Sets whether to run skeleton analysis in verbose mode.

setVerbose(boolean) - Method in class sc.fiji.snt.tracing.auto.ComponentReconnector

Enables or disables verbose logging.

setVertexColor(BrainAnnotation, ColorRGB) - Method in class sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter

setVertexColor(SWCPoint, ColorRGB) - Method in class sc.fiji.snt.viewer.geditor.TreeGraphAdapter

setVertexColor(V, ColorRGB) - Method in class sc.fiji.snt.analysis.graph.SNTGraph

setVertexColor(V, ColorRGB) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphAdapter

setVertexColor(V, ColorRGB) - Method in class sc.fiji.snt.viewer.geditor.SNTPseudographAdapter

setVertexValue(V, double) - Method in class sc.fiji.snt.analysis.graph.SNTGraph

setView(int) - Method in class sc.fiji.snt.analysis.RoiConverter

Sets the exporting view for segment paths (XY by default).

setViewMode(String) - Method in class sc.fiji.snt.viewer.Viewer3D

Renders the scene from a specified camera angle (script-friendly).

setViewMode(Viewer3D.ViewMode) - Method in class sc.fiji.snt.viewer.MultiViewer3D

setViewMode(Viewer3D.ViewMode) - Method in class sc.fiji.snt.viewer.Viewer3D

Renders the scene from a specified camera angle.

setViewPoint(double, double) - Method in class sc.fiji.snt.viewer.Viewer3D

Renders the scene from a specified camera angle using polar coordinates relative to the center of the scene.

setViewPointCC(double, double) - Method in class sc.fiji.snt.viewer.Viewer3D

Calls Viewer3D.setViewPoint(double, double) using Cartesian coordinates.

setViewTypeDetails() - Method in class sc.fiji.snt.gui.FileChooser

Sets the file view type to "details".

setViewTypeList() - Method in class sc.fiji.snt.gui.FileChooser

Sets the file view type to "list".

setVisibilityFilter(String, boolean) - Method in class sc.fiji.snt.SNTUI

Sets filters for visibility of paths, as per respective widget in dialog.

setVisible(boolean) - Method in class sc.fiji.snt.analysis.SNTChart

Deprecated.

setVisible(boolean) - Method in class sc.fiji.snt.gui.MeasureUI

setVisible(boolean) - Method in class sc.fiji.snt.gui.SNTCommandFinder

setVisible(boolean) - Method in class sc.fiji.snt.seed.SeedOverlay

Sets visibility; fires listeners if the value changed.

setVisible(boolean) - Method in class sc.fiji.snt.viewer.Bvv.AnnotationOverlay

Show/hide annotations

setVisible(String, boolean) - Method in class sc.fiji.snt.viewer.Viewer3D

Toggles the visibility of a rendered Tree, a loaded OBJ mesh, or an annotation.

setVolume(double) - Method in class sc.fiji.snt.viewer.OBJMesh

Sets the volume of this mesh.

setWarningOutlineEnabled(boolean) - Method in class sc.fiji.snt.gui.SearchField

setWaypointBiasFixedFactor(double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the fixed bias factor used when source is AbstractGWDTTracer.WaypointBiasSource.FIXED; clamped to [0, 1].

setWaypointBiasRadiusVoxels(double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the bias sphere radius in voxels; non-positive disables the spherical extent (only the exact waypoint voxel is biased).

setWaypointBiasSource(AbstractGWDTTracer.WaypointBiasSource) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets AbstractGWDTTracer.WaypointBiasSource; null resets to AbstractGWDTTracer.WaypointBiasSource.CONFIDENCE.

setWaypointBiasStrength(double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Sets the overall bias strength; values are clamped to [0, 1].

setWaypoints(Collection<SeedPoint>) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Configures the run's waypoints.

setWaypoints(Collection<SeedPoint>) - Method in interface sc.fiji.snt.tracing.auto.AutoTracer

Hands the tracer a collection of seeds to use as waypoints (path constraints) in this run.

setWidth(int) - Method in class sc.fiji.snt.analysis.PathStraightener

Sets the width of the straightened path image.

setWindowSizeFraction(double) - Method in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

Sets the window size fraction for change point detection.

setWireframeColor(String) - Method in class sc.fiji.snt.viewer.Annotation3D

Script friendly method to assign a wireframe color to the annotation.

setWireframeColor(ColorRGB) - Method in class sc.fiji.snt.viewer.Annotation3D

Assigns a wireframe color to the annotation.

setWorkspaceDir(File) - Method in class sc.fiji.snt.SNTPrefs

setX(int) - Method in class sc.fiji.snt.tracing.BiSearchNode

setXrange(double, double) - Method in class sc.fiji.snt.viewer.MultiViewer2D

Sets a manual range for the viewers' X-axis.

setXrange(double, double) - Method in class sc.fiji.snt.viewer.Viewer2D

Sets a manual range for the viewers' X-axis.

setY(int) - Method in class sc.fiji.snt.tracing.BiSearchNode

setYrange(double, double) - Method in class sc.fiji.snt.viewer.MultiViewer2D

Sets a manual range for the viewers' Y-axis.

setYrange(double, double) - Method in class sc.fiji.snt.viewer.Viewer2D

Sets a manual range for the viewers' Y-axis.

setZ(int) - Method in class sc.fiji.snt.tracing.BiSearchNode

setZFudge(double) - Method in class sc.fiji.snt.tracing.cost.OneMinusErf

Scale factor for intensity z-score.

setZigzagRemovalEnabled(boolean) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Enables or disables zigzag removal.

setZoom(double) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

setZPositionAllPanes(int, int, int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

severity() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCheck.Warning

Returns the value of the severity record component.

severityColor(PlausibilityCheck.Severity) - Static method in class sc.fiji.snt.CurationManager

SHADING_DEFAULT - Static variable in class sc.fiji.snt.viewer.OBJMesh

Shading mode: jzy3d fixed-function rendering (default).

SHADING_SMOOTH - Static variable in class sc.fiji.snt.viewer.OBJMesh

Shading mode: per-fragment Phong lighting with hemispherical ambient (GLSL 1.20).

SHELL - Static variable in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

shift(double[]) - Method in class sc.fiji.snt.util.BoundingBox

SHOLL_COUNTS - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Sholl inters. counts

SHOLL_DECAY - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Sholl: Decay" statistics

SHOLL_KURTOSIS - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Sholl: Kurtosis" statistics

SHOLL_MAX_FITTED - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Sholl: Max (fitted)" statistics

SHOLL_MAX_FITTED_RADIUS - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Sholl: Max (fitted) radius" statistics

SHOLL_MAX_VALUE - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying Sholl max statistics

SHOLL_MEAN_VALUE - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying Sholl mean statistics

SHOLL_N_MAX - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Sholl: No. maxima" statistics

SHOLL_N_SECONDARY_MAX - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Sholl: No. secondary maxima" statistics

SHOLL_POLY_FIT_DEGREE - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Sholl: Degree of Polynomial fit" statistics

SHOLL_RAMIFICATION_INDEX - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Sholl: Ramification index" statistics

SHOLL_SKEWNESS - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Sholl: Skewness" statistics

SHOLL_SUM_VALUE - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying Sholl sum statistics

shollAnalysis() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

ShollAnalysisBulkTreeCmd - Class in sc.fiji.snt.plugin

A modified version of ShollAnalysisTreeCmd for Bulk Sholl Analysis.

ShollAnalysisBulkTreeCmd() - Constructor for class sc.fiji.snt.plugin.ShollAnalysisBulkTreeCmd

ShollAnalysisImgCmd - Class in sc.fiji.snt.plugin

Command for performing Sholl analysis on binary 2D/3D images of neuronal structures.

ShollAnalysisImgCmd() - Constructor for class sc.fiji.snt.plugin.ShollAnalysisImgCmd

ShollAnalysisImgCommonCmd - Class in sc.fiji.snt.plugin

Implements the backbone for Analyze:Sholl:Sholl Analysis (From Image) commands...

ShollAnalysisImgCommonCmd() - Constructor for class sc.fiji.snt.plugin.ShollAnalysisImgCommonCmd

ShollAnalysisImgInteractiveCmd - Class in sc.fiji.snt.plugin

Interactive command for performing Sholl analysis on binary 2D/3D images, with real-time parameter adjustment and visualization updates.

ShollAnalysisImgInteractiveCmd() - Constructor for class sc.fiji.snt.plugin.ShollAnalysisImgInteractiveCmd

ShollAnalysisPrefsCmd - Class in sc.fiji.snt.plugin

Implements the "Sholl Options" command

ShollAnalysisPrefsCmd() - Constructor for class sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

ShollAnalysisTreeCmd - Class in sc.fiji.snt.plugin

Implements SNT's commands for Sholl Analysis of Trees.

ShollAnalysisTreeCmd() - Constructor for class sc.fiji.snt.plugin.ShollAnalysisTreeCmd

ShollAnalysisTreeInteractiveCmd - Class in sc.fiji.snt.plugin

Interactive command for performing Sholl analysis on reconstructed neuronal tracings, with real-time parameter adjustment and interactive visualization.

ShollAnalysisTreeInteractiveCmd() - Constructor for class sc.fiji.snt.plugin.ShollAnalysisTreeInteractiveCmd

ShollAnalyzer - Class in sc.fiji.snt.analysis

Class to retrieve Sholl metrics from a Tree.

ShollAnalyzer(Tree) - Constructor for class sc.fiji.snt.analysis.ShollAnalyzer

Instantiates a new Sholl analyzer using default settings, i.e., focused on Tree's root; using sampling step size of average inter-node distance; curve fitting enabled; and all other parameters left to defaults/auto-discovery.

ShollAnalyzer(Tree, TreeStatistics) - Constructor for class sc.fiji.snt.analysis.ShollAnalyzer

ShollOverlay - Class in sc.fiji.snt.analysis.sholl.gui

Renders Sholl analysis results as graphical overlays on an image, including concentric shells, sampling points, and intersection counts.

ShollOverlay(Profile) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

ShollOverlay(Profile, ImagePlus) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

ShollOverlay(Profile, ImagePlus, boolean) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

ShollPlot - Class in sc.fiji.snt.analysis.sholl.gui

An ImageJ Plot for displaying Sholl analysis profiles, including sampled data, fitted curves, and descriptive statistics.

ShollPlot(String, String, String) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollPlot

Constructs a new empty Plot.

ShollPlot(String, String, String, ShollStats, boolean, boolean) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollPlot

ShollPlot(ShollStats) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollPlot

ShollPlot(ShollStats.DataMode, Profile...) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollPlot

ShollPlot(ShollStats, boolean) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollPlot

ShollPlot(Profile) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollPlot

ShollPlot(Profile...) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollPlot

ShollPoint - Class in sc.fiji.snt.util

Convenience flavor of PointInImage defining 2D/3D points for Sholl Analysis.

ShollPoint(double, double) - Constructor for class sc.fiji.snt.util.ShollPoint

ShollPoint(double, double, double) - Constructor for class sc.fiji.snt.util.ShollPoint

ShollPoint(int, int, int, Calibration) - Constructor for class sc.fiji.snt.util.ShollPoint

ShollPoint(int, int, Calibration) - Constructor for class sc.fiji.snt.util.ShollPoint

ShollPoint(PointInImage) - Constructor for class sc.fiji.snt.util.ShollPoint

ShollStats - Interface in sc.fiji.snt.analysis.sholl.math

Methods and constants common to Profile analyzers.

ShollStats.DataMode - Enum Class in sc.fiji.snt.analysis.sholl.math

ShollTable - Class in sc.fiji.snt.analysis.sholl.gui

Implementation of SNTTable for Sholl metrics and Profile lists.

ShollTable() - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollTable

Instantiates a new empty table.

ShollTable(ShollStats...) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollTable

Instantiates a new table capable of detailing metrics from a LinearProfileStats, a NormalizedProfileStats instance or both.

ShollTable(Profile) - Constructor for class sc.fiji.snt.analysis.sholl.gui.ShollTable

Instantiates a new table from a Profile

ShollUtils - Class in sc.fiji.snt.analysis.sholl

Static utilities.

ShortcutWindowCmd - Class in sc.fiji.snt.gui.cmds

A command that displays a shortcut window of most popular commands, inspired by the Bio-Formats Plugins Shortcut Window.

ShortcutWindowCmd() - Constructor for class sc.fiji.snt.gui.cmds.ShortcutWindowCmd

SHORTEST_BRANCH - Static variable in class sc.fiji.snt.tracing.auto.BinaryTracer

Pruning mode: flag for shortest branch pruning

SHORTEST_EDGE - Static variable in class sc.fiji.snt.tracing.auto.BinaryTracer

Pruning mode: flag for shortest edge pruning (preserves longest paths).

shortSmallMsg(String) - Static method in class sc.fiji.snt.gui.GuiUtils

shortSmallMsg(String, boolean) - Static method in class sc.fiji.snt.gui.GuiUtils

show() - Method in class sc.fiji.snt.analysis.graph.AnnotationGraph

Displays this graph in a new instance of SNT's "Dendrogram Viewer".

show() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Displays this graph in a new instance of SNT's "Dendrogram Viewer".

show() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph

Displays this graph in a new instance of SNT's "Dendrogram Viewer".

show() - Method in class sc.fiji.snt.analysis.SNTChart

show() - Method in class sc.fiji.snt.analysis.SNTTable

Displays the table in a window.

show() - Method in class sc.fiji.snt.gui.CostPalette

show() - Method in class sc.fiji.snt.Tree

Displays this Tree in an appropriate viewer (3D if the tree has depth, 2D otherwise).

show() - Method in class sc.fiji.snt.viewer.GraphViewer

Displays a graph in SNT's "Graph Viewer" featuring UI commands for interactive visualization and export options.

show() - Method in class sc.fiji.snt.viewer.MultiViewer2D

show() - Method in class sc.fiji.snt.viewer.MultiViewer3D

show() - Method in class sc.fiji.snt.viewer.Viewer2D

Displays the current plot on a dedicated frame

show() - Method in class sc.fiji.snt.viewer.Viewer3D

Displays the Viewer and returns a reference to its frame.

show(int, int) - Method in class sc.fiji.snt.analysis.SNTChart

Shows this chart on a dedicated frame

show(int, int) - Method in class sc.fiji.snt.viewer.Viewer2D

Displays the current plot on a dedicated frame *

show(int, int) - Method in class sc.fiji.snt.viewer.Viewer3D

Displays the viewer under specified dimensions.

show(ImagePlus) - Method in class sc.fiji.snt.viewer.Bvv

Displays the BVV viewer with the specified image.

show(Color) - Static method in class sc.fiji.snt.gui.GuiUtils.Buttons

show(Object) - Static method in class sc.fiji.snt.viewer.Viewer3D

Convenience factory that creates a viewer, adds the given object, and displays it.

show(String) - Method in class sc.fiji.snt.analysis.SNTChart

show(String) - Method in class sc.fiji.snt.analysis.SNTTable

show(String) - Method in class sc.fiji.snt.viewer.GraphViewer

Displays a graph in SNT's "Graph Viewer" featuring UI commands for interactive visualization and export options.

show(List<RandomAccessibleInterval<T>>, List<double[]>) - Method in class sc.fiji.snt.viewer.Bvv

Displays a list of RandomAccessibleInterval volumes, each as a BvvMultiSource.

show(List<ShollPlot>, String) - Static method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

show(AbstractSpimData<?>) - Method in class sc.fiji.snt.viewer.Bvv

Displays a AbstractSpimData dataset using BVV's pyramid-aware GPU cache manager.

show(ImgPlus<T>) - Method in class sc.fiji.snt.viewer.Bvv

show(RandomAccessibleInterval<T>, double...) - Method in class sc.fiji.snt.viewer.Bvv

Displays the BVV viewer with the specified image.

show(DirectedWeightedGraph) - Static method in class sc.fiji.snt.analysis.graph.GraphUtils

Displays a graph in SNT's "Dendrogram Viewer" featuring UI commands for interactive visualization and export options.

show2D() - Method in class sc.fiji.snt.Tree

Displays this Tree in Viewer2D.

show3D() - Method in class sc.fiji.snt.Tree

Displays this Tree in Viewer3D.

showAboutDialog() - Static method in class sc.fiji.snt.gui.GuiUtils

showCanvasInfo(String) - Method in class sc.fiji.snt.SNT

showCanvasInfo(String, int) - Method in class sc.fiji.snt.SNT

Displays a timed informational message (blue background) on the canvas banner.

showCanvasWarning(String) - Method in class sc.fiji.snt.SNT

showCanvasWarning(String, int) - Method in class sc.fiji.snt.SNT

Displays a timed warning (amber background) on the canvas banner.

ShowCorrespondencesCmd - Class in sc.fiji.snt.gui.cmds

Command for highlighting the correspondences between two reconstructions in the Legacy 3D Viewer

ShowCorrespondencesCmd() - Constructor for class sc.fiji.snt.gui.cmds.ShowCorrespondencesCmd

showCorrespondencesTo(File, Color, double) - Method in class sc.fiji.snt.SNT

Deprecated.

showDialog(Component, String) - Method in class sc.fiji.snt.gui.OntologyBrowser

Shows this browser in a modal dialog and returns the selected paths, or null if the user cancelled.

showDirectory(File) - Method in class sc.fiji.snt.gui.GuiUtils

showHeatmap(double[][], ColorTable, String...) - Static method in class sc.fiji.snt.analysis.SNTChart

Shows a two-dimensional heatmap from a two-dimensional data matrix.

showHeatmap(Collection<Double>, Collection<Double>, ColorTable, String...) - Static method in class sc.fiji.snt.analysis.SNTChart

Shows a two-dimensional heatmap for a two-dimensional data matrix assembled from two collections

showHelpOnCountingSpines(Component, Runnable) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

showHint(String) - Method in class sc.fiji.snt.gui.GuiUtils

showHistogram3D(double[][], ColorTable, boolean, String...) - Static method in class sc.fiji.snt.analysis.SNTChart

Shows a bivariate histogram (two-dimensional histogram) from a matrix.

showHistogram3D(Collection<Double>, Collection<Double>, ColorTable, String...) - Static method in class sc.fiji.snt.analysis.SNTChart

Shows a bivariate histogram (two-dimensional histogram) from two collections of values.

showHistogram3D(DescriptiveStatistics, DescriptiveStatistics, ColorTable, String...) - Static method in class sc.fiji.snt.analysis.SNTChart

Shows a bivariate histogram (two-dimensional histogram) from two DescriptiveStatistics objects.

showHTMLDialog(String, String) - Static method in class sc.fiji.snt.gui.GuiUtils

showHTMLDialog(String, String, boolean) - Method in class sc.fiji.snt.gui.GuiUtils

showKeyboardShortcuts(InputMap[], ActionMap...) - Method in class sc.fiji.snt.gui.GuiUtils

Displays a sorted HTML table of all registered keyboard shortcuts in the specified inputMaps.

showLoadedData() - Method in class sc.fiji.snt.viewer.Bvv

Displays the main tracing data from the associated SNT instance.

showMessage(String, String) - Method in class sc.fiji.snt.SNT

showMessage(String, String) - Method in class sc.fiji.snt.SNTUI

showMIPOverlays(boolean, double) - Method in class sc.fiji.snt.SNT

showMIPOverlays(double) - Method in class sc.fiji.snt.SNT

Overlays a semi-transparent MIP (8-bit scaled) of the data being traced over the tracing canvas(es).

showModelessDialog(Component, String) - Method in class sc.fiji.snt.gui.OntologyBrowser

Shows this browser in a modeless (non-modal) dialog for reference browsing.

showMouseThreshold(double) - Method in class sc.fiji.snt.FillManagerUI

showOnlyActiveCTposPaths - Variable in class sc.fiji.snt.SNT

showOnlySelectedPaths - Variable in class sc.fiji.snt.SNT

showPanel() - Method in class sc.fiji.snt.BookmarkManager

Alias for BookmarkManager.toggleBvvPanel() shows the marker panel.

showPlot() - Method in class sc.fiji.snt.viewer.Viewer2D

Deprecated.

Use Viewer2D.show() instead.

showProgress(int, int) - Method in class sc.fiji.snt.viewer.Viewer3D.ManagerPanel

Updates the progress bar.

showScrollableDialog() - Method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

Adds AWT scroll bars to the dialog before displaying it, when not running headless.

showSecondaryData() - Method in class sc.fiji.snt.viewer.Bvv

Displays the secondary tracing data from the associated SNT instance.

showSelectionInfo(Component) - Method in class sc.fiji.snt.gui.OntologyBrowser

Displays an HTML info table for the currently checked compartments.

showStatus(int, int, String) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

showStatus(int, int, String) - Method in interface sc.fiji.snt.hyperpanes.PaneOwner

Shows a status message with progress information.

showStatus(int, int, String) - Method in class sc.fiji.snt.SNT

showStatus(String, boolean) - Method in class sc.fiji.snt.SNTUI

Updates the status bar.

SHUFFLE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

SIDE - Enum constant in enum class sc.fiji.snt.viewer.Viewer3D.ViewMode

Deprecated.

Use YZ instead

SigmaPalette - Class in sc.fiji.snt.gui

Implements SNT 'Sigma wizard'.

SigmaPalette(SNT) - Constructor for class sc.fiji.snt.gui.SigmaPalette

SigmaPaletteListener - Interface in sc.fiji.snt.gui

Listener interface for the sigma (gaussian blur standard deviation) palette.

SigmaUtils - Class in sc.fiji.snt.util

Utility class for computing default Gaussian blur sigma values based on image properties.

SignalQuality() - Constructor for class sc.fiji.snt.analysis.curation.PlausibilityCheck.SignalQuality

SIGNS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

simplifiedString(BrainAnnotation) - Static method in interface sc.fiji.snt.annotation.BrainAnnotation

single_pane - Variable in class sc.fiji.snt.hyperpanes.MultiDThreePanes

singleSlice - Variable in class sc.fiji.snt.hyperpanes.MultiDThreePanes

size - Variable in class sc.fiji.snt.analysis.AbstractConvexHull

size() - Method in class sc.fiji.snt.analysis.AbstractConvexHull

Returns the area (2D) or volume (3D) of this convex hull.

size() - Method in class sc.fiji.snt.analysis.ConvexHull2D

size() - Method in class sc.fiji.snt.analysis.ConvexHull3D

size() - Method in class sc.fiji.snt.analysis.sholl.Profile

size() - Method in class sc.fiji.snt.Path

Returns the number of nodes of this path

size() - Method in class sc.fiji.snt.PathAndFillManager

Returns the number of Paths in the PathAndFillManager list.

size() - Method in class sc.fiji.snt.seed.SeedOverlay

size() - Method in class sc.fiji.snt.tracing.image.SearchImageStack

size() - Method in class sc.fiji.snt.Tree

Retrieves the number of paths in this tree.

size() - Method in class sc.fiji.snt.viewer.BvvMultiSource

SIZE - Static variable in class sc.fiji.snt.analysis.ConvexHullAnalyzer

sizes() - Method in record class sc.fiji.snt.io.OmeAxisUtils.OmeMetadata

Returns the value of the sizes record component.

skeletonize(ImagePlus, boolean) - Static method in class sc.fiji.snt.tracing.auto.BinaryTracer

Convenience method to skeletonize a thresholded image using Skeletonize3D_.

skeletonize(ImagePlus, double, double, boolean) - Static method in class sc.fiji.snt.tracing.auto.BinaryTracer

Convenience method to skeletonize an image using Skeletonize3D_.

skeletonize(ImagePlus, int) - Method in class sc.fiji.snt.Tree

Skeletonizes (rasterizes) this tree on the specified image using Bresenham’s Algorithm (3D).

SkeletonizerCmd - Class in sc.fiji.snt.plugin

Convenience command for converting Paths into skeleton images

SkeletonizerCmd() - Constructor for class sc.fiji.snt.plugin.SkeletonizerCmd

skeletonizeTimeLapse(ImagePlus, boolean) - Static method in class sc.fiji.snt.tracing.auto.BinaryTracer

Convenience method to skeletonize a thresholded time-lapse using Skeletonize3D_.

skipDiameterForDirectionArrows() - Method in class sc.fiji.snt.PathNodeCanvas

Checks if direction arrows are enabled and this node should skip diameter rendering.

SLAB - Static variable in class sc.fiji.snt.PathNodeCanvas

Flag describing a slab node

SliceResult(ImgPlus<T>, int, int) - Constructor for record class sc.fiji.snt.util.ImgUtils.SliceResult

Creates an instance of a SliceResult record class.

SLIDERS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

smallButton(String) - Static method in class sc.fiji.snt.gui.GuiUtils.Buttons

smoothCurve(DirectedWeightedGraph, int) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Smooths the final curve using a moving average filter.

smoothEnabled - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

smoothWindowSize - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

snapCursor - Variable in class sc.fiji.snt.SNT

snapshot() - Method in class sc.fiji.snt.viewer.Bvv

Retrieves the current scene as an image.

snapshot() - Method in class sc.fiji.snt.viewer.Viewer3D

Retrieves the current scene as an image

snapshot(String) - Method in class sc.fiji.snt.viewer.Bvv

Retrieves the specified scene view as an image.

snapshot(String) - Method in class sc.fiji.snt.viewer.Viewer3D

Retrieves the specified scene view as an image.

snapshotWYSIWYG() - Method in class sc.fiji.snt.viewer.Viewer3D

Retrieves the current scene as an image using a screen capture that matches the on-screen rendering exactly (WYSIWYG).

snapWindowXYsizeSpinner - Variable in class sc.fiji.snt.SNTUI

snapWindowZsizeSpinner - Variable in class sc.fiji.snt.SNTUI

snt - Variable in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

SNT - Class in sc.fiji.snt

Implements the SNT plugin.

SNT(ImagePlus) - Constructor for class sc.fiji.snt.SNT

Script-friendly constructor for Instantiating and initializing SNT in 'Tracing Mode' (typically headless operations).

SNT(ImgPlus<T>) - Constructor for class sc.fiji.snt.SNT

Script-friendly constructor for Instantiating SNT in 'Tracing Mode' (typically headless operations)

SNT(ImgPlus<T>, int, int) - Constructor for class sc.fiji.snt.SNT

Script-friendly constructor for Instantiating SNT in 'Tracing Mode' (typically headless operations)

SNT(Context, ImagePlus) - Constructor for class sc.fiji.snt.SNT

Instantiates SNT in 'Tracing Mode'.

SNT(Context, PathAndFillManager) - Constructor for class sc.fiji.snt.SNT

Instantiates SNT in 'Analysis Mode'

SNT_PAUSED - Static variable in class sc.fiji.snt.SNTUI

Flag specifying all SNT are temporarily disabled (all user interactions are waived back to ImageJ)

SNT.CostType - Enum Class in sc.fiji.snt

SNT.FilterType - Enum Class in sc.fiji.snt

SNT.HeuristicType - Enum Class in sc.fiji.snt

SNT.SearchImageType - Enum Class in sc.fiji.snt

SNT.SearchType - Enum Class in sc.fiji.snt

SNTChart - Class in sc.fiji.snt.analysis

Extension of ChartPanel modified for scientific publications and convenience methods for plot annotations.

SNTChart(String, JFreeChart) - Constructor for class sc.fiji.snt.analysis.SNTChart

SNTChart(String, JFreeChart, Dimension) - Constructor for class sc.fiji.snt.analysis.SNTChart

SNTChart(String, CategoryChart) - Constructor for class sc.fiji.snt.analysis.SNTChart

SNTChart(String, XYPlot) - Constructor for class sc.fiji.snt.analysis.SNTChart

SNTColor - Class in sc.fiji.snt.util

A simple class for handling Colors including the ability to map an AWT Color to a SWC type integer tag.

SNTColor(Color) - Constructor for class sc.fiji.snt.util.SNTColor

Instantiates a new SNT color without SWC type association

SNTColor(Color, int) - Constructor for class sc.fiji.snt.util.SNTColor

Instantiates a new SNT color.

SNTCommandFinder - Class in sc.fiji.snt.gui

Implements SNT's Command Palette.

SNTCommandFinder(SNTUI) - Constructor for class sc.fiji.snt.gui.SNTCommandFinder

Constructs a new SNTCommandFinder for the specified SNTUI instance.

SNTCommandFinder(Viewer3D) - Constructor for class sc.fiji.snt.gui.SNTCommandFinder

Constructs a new SNTCommandFinder for the specified Viewer3D instance.

SNTEditorPane - Class in sc.fiji.snt.gui

Implements minor customizations to EditorPane for usage by SNT.

SNTEditorPane(boolean) - Constructor for class sc.fiji.snt.gui.SNTEditorPane

SNTEvent - Class in sc.fiji.snt.event

Base event class for SNT events.

SNTEvent(int) - Constructor for class sc.fiji.snt.event.SNTEvent

Constructs a new SNT event with the specified type.

SNTGraph<V,E> - Class in sc.fiji.snt.analysis.graph

An abstract weighted graph implementation that extends AbstractBaseGraph with additional support for vertex/edge coloring and vertex value mapping.

SNTGraph(Supplier<V>, Supplier<E>, GraphType) - Constructor for class sc.fiji.snt.analysis.graph.SNTGraph

SNTGraph(Supplier<V>, Supplier<E>, GraphType, GraphSpecificsStrategy<V, E>) - Constructor for class sc.fiji.snt.analysis.graph.SNTGraph

Variant constructor that lets a subclass pick a custom GraphSpecificsStrategy: e.g. a CSR-backed implementation to keep memory usage proportional to (V+E) rather than to the per-vertex object overhead jgrapht's default strategies use.

SNTGraphAdapter<V,E> - Class in sc.fiji.snt.viewer.geditor

Base adapter that converts SNT graphs to JGraphX graph models for visualization.

SNTGraphAdapter(SNTGraph<V, E>) - Constructor for class sc.fiji.snt.viewer.geditor.SNTGraphAdapter

SNTGraphComponent - Class in sc.fiji.snt.viewer.geditor

Base JGraphX component for SNT graph visualization with interactive controls.

SNTGraphComponent(SNTGraphAdapter<?, ? extends DefaultWeightedEdge>, Context) - Constructor for class sc.fiji.snt.viewer.geditor.SNTGraphComponent

SNTInterpreterPane - Class in sc.fiji.snt.gui

SNT's interpreter UI pane.

SNTInterpreterPane(Context, String) - Constructor for class sc.fiji.snt.gui.SNTInterpreterPane

SNTInterpreterWindow - Class in sc.fiji.snt.gui

SNT's REPL window.

SNTInterpreterWindow(Context, String) - Constructor for class sc.fiji.snt.gui.SNTInterpreterWindow

SNTListener - Interface in sc.fiji.snt.event

Listener interface for SNT events.

SNTLoaderCmd - Class in sc.fiji.snt.gui.cmds

Command for Launching SNT

SNTLoaderCmd() - Constructor for class sc.fiji.snt.gui.cmds.SNTLoaderCmd

SNTPoint - Interface in sc.fiji.snt.util

Classes extend this interface implement a point in a 3D space, always using real world coordinates.

SNTPrefs - Class in sc.fiji.snt

Class handling SNT preferences.

SNTPrefs(SNT) - Constructor for class sc.fiji.snt.SNTPrefs

Constructs a new SNTPrefs instance for the specified SNT instance.

SNTPromptPane - Class in sc.fiji.snt.gui

Syntax-highlighted prompt pane for the SNT scripting REPL.

SNTPromptPane(ScriptREPL, VarsPane, OutputPane) - Constructor for class sc.fiji.snt.gui.SNTPromptPane

SNTPseudograph<V,E> - Class in sc.fiji.snt.analysis.graph

A specialized implementation of SNTGraph that represents a directed pseudograph with weighted edges.

SNTPseudograph(Class<? extends E>) - Constructor for class sc.fiji.snt.analysis.graph.SNTPseudograph

Constructs a new SNTPseudograph with edges of the specified class.

SNTPseudographAdapter<V,E> - Class in sc.fiji.snt.viewer.geditor

JGraphX adapter for visualizing SNT pseudographs (graphs allowing self-loops and multiple edges).

SNTPseudographAdapter(SNTPseudograph<V, E>) - Constructor for class sc.fiji.snt.viewer.geditor.SNTPseudographAdapter

SNTPseudographComponent - Class in sc.fiji.snt.viewer.geditor

JGraphX visualization component for SNT pseudographs.

SNTPseudographComponent(SNTPseudographAdapter<?, ? extends DefaultWeightedEdge>, Context) - Constructor for class sc.fiji.snt.viewer.geditor.SNTPseudographComponent

SNTREPL - Class in sc.fiji.snt.gui

SNT's Groovy REPL.

SNTREPL(Context) - Constructor for class sc.fiji.snt.gui.SNTREPL

SNTSearchableBar - Class in sc.fiji.snt.gui

Implements a SearchableBar following SNT's UI.

SNTSearchableBar(Searchable) - Constructor for class sc.fiji.snt.gui.SNTSearchableBar

SNTSearchableBar(Searchable, String) - Constructor for class sc.fiji.snt.gui.SNTSearchableBar

sntService - Variable in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

sntService - Variable in class sc.fiji.snt.gui.cmds.PrefsCmd

SNTService - Class in sc.fiji.snt

Service for accessing and scripting the active instance of SNT.

SNTService() - Constructor for class sc.fiji.snt.SNTService

SNTTable - Class in sc.fiji.snt.analysis

Extension of DefaultGenericTable with (minor) scripting conveniences.

SNTTable() - Constructor for class sc.fiji.snt.analysis.SNTTable

SNTTable(String) - Constructor for class sc.fiji.snt.analysis.SNTTable

SNTTable(String, char) - Constructor for class sc.fiji.snt.analysis.SNTTable

SNTTable(Map<String, Collection<Number>>) - Constructor for class sc.fiji.snt.analysis.SNTTable

SNTUI - Class in sc.fiji.snt

Implements SNT's main dialog.

SNTUI(SNT) - Constructor for class sc.fiji.snt.SNTUI

Instantiates SNT's main UI and associated PathManagerUI and FillManagerUI instances.

SNTUtils - Class in sc.fiji.snt

Static utilities for SNT

SOMA - Static variable in class sc.fiji.snt.io.MouseLightLoader

The Constant SOMA.

SOMA_RENDER_DEFAULT - Static variable in class sc.fiji.snt.PathNodeCanvas

Soma rendering mode: filled circle scaled to actual radius

SOMA_RENDER_TRIANGLE - Static variable in class sc.fiji.snt.PathNodeCanvas

Soma rendering mode: triangle scaled to actual radius (only for SWC_SOMA tagged paths)

SomaDetectorCmd - Class in sc.fiji.snt.plugin

Command to automatically detect the soma (cell body) in neuronal images.

SomaDetectorCmd() - Constructor for class sc.fiji.snt.plugin.SomaDetectorCmd

SomaDistance() - Constructor for class sc.fiji.snt.analysis.curation.PlausibilityCheck.SomaDistance

SomaResult(long[], double[], Img<BitType>, Polygon, double, double, int, String) - Constructor for record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Creates an instance of a SomaResult record class.

somaRoi - Variable in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Soma ROI Strategies - Search tag in package sc.fiji.snt.tracing.auto

Section

somaRoiZPosition - Variable in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

SOMATIC - Static variable in interface sc.fiji.snt.TreeProperties

SomaUtils - Class in sc.fiji.snt.tracing.auto

Utilities for automatic soma detection and ROI generation.

SomaUtils.SomaResult - Record Class in sc.fiji.snt.tracing.auto

Container for soma detection results.

somehowJoinsAsString() - Method in class sc.fiji.snt.Path

SORT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

sortedMappedTrees() - Method in class sc.fiji.snt.analysis.MultiTreeColorMapper

sortVertices() - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutGrouped

sortVertices(Object[], String) - Method in class sc.fiji.snt.viewer.geditor.mxCircleLayoutSorted

source - Variable in class sc.fiji.snt.seed.SeedPoint

Provenance label (e.g.

source - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

source() - Method in class sc.fiji.snt.analysis.sholl.Profile

source() - Method in record class sc.fiji.snt.io.OmeAxisUtils.OmeMetadata

Returns the value of the source record component.

SOURCE - Enum constant in enum class sc.fiji.snt.seed.SeedOverlay.ColorMode

SOURCE_ALL - Static variable in class sc.fiji.snt.plugin.AutotraceFromTipsCmd

SOURCE_SELECTION - Static variable in class sc.fiji.snt.plugin.AutotraceFromBinarySeedsCmd

SOURCE_SELECTION - Static variable in class sc.fiji.snt.plugin.AutotraceFromBinaryTipsCmd

SOURCE_SELECTION - Static variable in class sc.fiji.snt.plugin.AutotraceFromSeedsCmd

SOURCE_SELECTION - Static variable in class sc.fiji.snt.plugin.AutotraceFromTipsCmd

SOURCE_SELECTION - Static variable in class sc.fiji.snt.plugin.AutotraceFromWaypointsCmd

SOURCE_VISIBLE - Static variable in class sc.fiji.snt.plugin.AutotraceFromTipsCmd

spacing - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

spacing(double[]) - Method in class sc.fiji.snt.analysis.detection.LabelProximityDetector.Config

Sets explicit pixel spacing for the EDT computation.

spacing_units - Variable in class sc.fiji.snt.Fill

spacing_units - Variable in class sc.fiji.snt.Path

spacing_units - Variable in class sc.fiji.snt.SNT

spacing_units - Variable in class sc.fiji.snt.tracing.AbstractSearch

spacing_units - Variable in class sc.fiji.snt.tracing.TubularGeodesicsTracer

spacingUnit - Variable in class sc.fiji.snt.util.BoundingBox

spacingUnits() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Returns the value of the spacingUnits record component.

SparseDirectedWeightedGraph - Class in sc.fiji.snt.analysis.graph

Memory-efficient variant of DirectedWeightedGraph backed by a compressed sparse-row (CSR) adjacency representation (CsrDirectedSpecifics).

SparseDirectedWeightedGraph() - Constructor for class sc.fiji.snt.analysis.graph.SparseDirectedWeightedGraph

Creates an empty sparse directed-weighted graph.

SparseDirectedWeightedGraph(Collection<SWCPoint>, boolean) - Constructor for class sc.fiji.snt.analysis.graph.SparseDirectedWeightedGraph

Builds a CSR-backed graph from a collection of SWC nodes.

SparseDirectedWeightedGraph(Tree) - Constructor for class sc.fiji.snt.analysis.graph.SparseDirectedWeightedGraph

Builds a CSR-backed graph from a Tree.

SparseDirectedWeightedGraph(Tree, boolean) - Constructor for class sc.fiji.snt.analysis.graph.SparseDirectedWeightedGraph

Builds a CSR-backed graph from a Tree, with an option to skip Euclidean edge-weight assignment.

SparseGWDTTracer<T> - Class in sc.fiji.snt.tracing.auto

Sparse GWDT tracer using hash map storage for memory efficiency.

SparseGWDTTracer(ImagePlus) - Constructor for class sc.fiji.snt.tracing.auto.SparseGWDTTracer

Creates a new SparseGWDTTracer from an ImagePlus.

SparseGWDTTracer(ImgPlus<T>) - Constructor for class sc.fiji.snt.tracing.auto.SparseGWDTTracer

Creates a new SparseGWDTTracer from an ImgPlus.

SparseGWDTTracer(RandomAccessibleInterval<T>) - Constructor for class sc.fiji.snt.tracing.auto.SparseGWDTTracer

Creates a new SparseGWDTTracer with isotropic spacing (1.0 for each dimension).

SparseGWDTTracer(RandomAccessibleInterval<T>, double[]) - Constructor for class sc.fiji.snt.tracing.auto.SparseGWDTTracer

Creates a new SparseGWDTTracer.

SparseStorageBackend - Class in sc.fiji.snt.tracing.auto.gwdt

Sparse storage backend using hash maps for memory-efficient tracing.

SparseStorageBackend(long[]) - Constructor for class sc.fiji.snt.tracing.auto.gwdt.SparseStorageBackend

spatialCalibration() - Method in class sc.fiji.snt.analysis.sholl.Profile

SPECTRAL - Enum constant in enum class sc.fiji.snt.SNT.FilterType

SpectralSimilarity<T,U> - Class in sc.fiji.snt.filter

Computes a spectral similarity map from a multichannel (e.g., Brainbow) image.

SpectralSimilarity(double[], int) - Constructor for class sc.fiji.snt.filter.SpectralSimilarity

Constructs a spectral similarity filter.

SpectralSimilarity(double[], int, double) - Constructor for class sc.fiji.snt.filter.SpectralSimilarity

Constructs a spectral similarity filter with custom intensity tolerance.

SPHERE - Static variable in class sc.fiji.snt.analysis.PathProfiler

sphereOverlapThreshold - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

SpimDataUtils - Class in sc.fiji.snt.io

Utilities for working with AbstractSpimData and BigDataViewer XML descriptors.

SpimDataUtils.CalibratedSource<T> - Class in sc.fiji.snt.io

Wraps a RandomAccessibleIntervalSource and overrides SpimDataUtils.CalibratedSource.getVoxelDimensions() to carry the physical unit (e.g.

SPINNER - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

SPLIT_FILLS_KEY - Static variable in class sc.fiji.snt.SNTPrefs

splitAtSomaBoundary(DirectedWeightedGraph) - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Splits a graph at the soma boundary, creating separate trees for each neurite.

splitByHemisphere(DirectedWeightedGraph) - Static method in class sc.fiji.snt.annotation.AllenUtils

splitByPrimaryPaths(Tree) - Static method in class sc.fiji.snt.util.TreeUtils

Splits a tree with multiple primary paths into separate trees, one rooted at each primary path.

splitIntoBlocks(RandomAccessibleInterval<T>, long[]) - Static method in class sc.fiji.snt.util.ImgUtils

Partition the source rai into a list of IntervalView with given dimensions.

SplitPanes() - Constructor for class sc.fiji.snt.gui.GuiUtils.SplitPanes

SpotSpineLoaderCmd - Class in sc.fiji.snt.gui.cmds

Implements the 'Open Spot Spine...' command.

SpotSpineLoaderCmd() - Constructor for class sc.fiji.snt.gui.cmds.SpotSpineLoaderCmd

SQUARE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

SRC_IMG - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

SRC_TABLE - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

SRC_TRACES - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

srRatio - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

STAIRS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

start - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

START - Static variable in class sc.fiji.snt.PathNodeCanvas

Flag describing a start point node

start_x - Variable in class sc.fiji.snt.tracing.BiSearch

start_x_image - Variable in class sc.fiji.snt.tracing.TubularGeodesicsTracer

start_y - Variable in class sc.fiji.snt.tracing.BiSearch

start_y_image - Variable in class sc.fiji.snt.tracing.TubularGeodesicsTracer

start_z - Variable in class sc.fiji.snt.tracing.BiSearch

start_z_image - Variable in class sc.fiji.snt.tracing.TubularGeodesicsTracer

startApp() - Static method in class sc.fiji.snt.SNTUtils

Convenience method to start up SNT's GUI.

startBallName - Static variable in class sc.fiji.snt.SNT

STARTED - Enum constant in enum class sc.fiji.snt.FillManagerUI.State

started_at - Variable in class sc.fiji.snt.tracing.SearchThread

startElement(String, String, String, Attributes) - Method in class sc.fiji.snt.PathAndFillManager

startFilling() - Method in class sc.fiji.snt.SNT

startFrame() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.ElongationEvent

Returns the value of the startFrame record component.

startFrame() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.RetractionEvent

Returns the value of the startFrame record component.

startHessian(String, double, double, boolean) - Method in class sc.fiji.snt.SNT

Deprecated.

startHessian(String, String, double[], double, double, String, int) - Method in class sc.fiji.snt.SNT

Constructs and enables an instance of a hessian eigenvalue filter.

startHessian(String, String, double[], String, int) - Method in class sc.fiji.snt.SNT

Constructs and enables an instance of a hessian eigenvalue filter.

startIndex() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhase

Returns the value of the startIndex record component.

startLength() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.ElongationEvent

Returns the value of the startLength record component.

startLength() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.RetractionEvent

Returns the value of the startLength record component.

startRadius() - Method in class sc.fiji.snt.analysis.sholl.Profile

startRubberBandSearch(double, double, int) - Method in class sc.fiji.snt.SNT

startSholl(PointInImage) - Method in class sc.fiji.snt.SNT

startTime() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.ElongationEvent

Returns the value of the startTime record component.

startTime() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhase

Returns the value of the startTime record component.

startTime() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.RetractionEvent

Returns the value of the startTime record component.

startUI() - Method in class sc.fiji.snt.SNT

status(String) - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Sends a status message to the registered listener, if any.

status(String) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

status(String, boolean) - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

status(String, boolean) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

STATUS_COVERED - Static variable in class sc.fiji.snt.seed.SeedTableModel

Cell value when a seed has a path node within tolerance.

STATUS_UNCOVERED - Static variable in class sc.fiji.snt.seed.SeedTableModel

Cell value when no path node lies within tolerance.

STATUS_UNKNOWN - Static variable in class sc.fiji.snt.seed.SeedTableModel

Cell value when there's no tracing context to compute against.

statusBar - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor

statusService - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

statusService - Variable in class sc.fiji.snt.analysis.TreeStatistics

statusService - Variable in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

statusService - Variable in class sc.fiji.snt.SNT

stdDev() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCalibrator.CheckSummary

Returns the value of the stdDev record component.

stdGrowthRate() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalysisResults.GrowthSummaryStatistics

Returns the value of the stdGrowthRate record component.

stdTotalGrowth() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalysisResults.GrowthSummaryStatistics

Returns the value of the stdTotalGrowth record component.

STEADY - Enum constant in enum class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhaseType

Steady phase - medium growth

stepSize() - Method in class sc.fiji.snt.analysis.sholl.Profile

STETHOSCOPE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

stopFilling() - Method in class sc.fiji.snt.SNT

stopFilling(boolean) - Method in class sc.fiji.snt.SNT

STOPPED - Enum constant in enum class sc.fiji.snt.FillManagerUI.State

storage - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

StorageBackend - Interface in sc.fiji.snt.tracing.auto.gwdt

Storage backend for GWDT tracing data structures.

Strahler - Class in sc.fiji.snt.plugin.ij1

This class implements the ImageJ Strahler Analysis plugin.

Strahler() - Constructor for class sc.fiji.snt.plugin.ij1.Strahler

STRAHLER_NUMBER - Static variable in class sc.fiji.snt.analysis.MultiTreeColorMapper

Mapping property: Horton-Strahler number

STRAHLER_NUMBER - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Horton-Strahler root number" statistics.

STRAHLER_ORDERS - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Horton-Strahler branch orders

STRAHLER_RATIO - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying Horton-Strahler bifurcation ratio statistics

strahlerAnalysis() - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

StrahlerAnalyzer - Class in sc.fiji.snt.analysis

Class to perform Horton-Strahler analysis on a Tree.

StrahlerAnalyzer(Tree) - Constructor for class sc.fiji.snt.analysis.StrahlerAnalyzer

StrahlerCmd - Class in sc.fiji.snt.plugin

Command to perform Horton-Strahler analysis on a collection of Trees

StrahlerCmd() - Constructor for class sc.fiji.snt.plugin.StrahlerCmd

Instantiates a new StrahlerCmd.

StrahlerCmd(Collection<Tree>) - Constructor for class sc.fiji.snt.plugin.StrahlerCmd

Instantiates a new StrahlerCmd.

StrahlerCmd(Tree) - Constructor for class sc.fiji.snt.plugin.StrahlerCmd

Instantiates a new StrahlerCmd for a single Tree

straighten() - Method in class sc.fiji.snt.analysis.PathStraightener

straighten(int) - Method in class sc.fiji.snt.analysis.PathStraightener

STREAM - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

STRIP - Static variable in class sc.fiji.snt.viewer.Annotation3D

stripExtension(String) - Static method in class sc.fiji.snt.SNTUtils

subFilteringEnabled - Variable in class sc.fiji.snt.gui.SNTSearchableBar

subgraph - Variable in class sc.fiji.snt.analysis.graph.GraphColorMapper

subInterval(RandomAccessibleInterval<T>, Localizable, Localizable, long) - Static method in class sc.fiji.snt.util.ImgUtils

Get an N-D sub-interval of an N-D image, given two corner points and specified padding.

subTree(int...) - Method in class sc.fiji.snt.Tree

Extracts the subset of paths matching the specified criteria.

subTree(String...) - Method in class sc.fiji.snt.Tree

Extracts the subset of paths matching the specified criteria (script friendly method)

subVolume(RandomAccessibleInterval<T>, long, long, long, long, long, long, long) - Static method in class sc.fiji.snt.util.ImgUtils

Get a 3D sub-volume of an image, given two corner points and specified padding.

succeeded() - Method in class sc.fiji.snt.analysis.MultiSpectralRefiner

Whether the refinement succeeded (penalty decreased or path was already optimal).

succeeded() - Method in class sc.fiji.snt.gui.SWCExportDialog

succeeded() - Method in class sc.fiji.snt.gui.SWCImportDialog

SUCCESS - Static variable in class sc.fiji.snt.tracing.SearchThread

successful() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

successful() - Method in interface sc.fiji.snt.analysis.sholl.parsers.Parser

Checks if the parsing operation was successful.

successful() - Method in class sc.fiji.snt.analysis.sholl.parsers.TabularParser

successful() - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

suggestRootLocation(Collection<Path>, PointInImage) - Static method in class sc.fiji.snt.util.TreeUtils

Analyzes paths and suggests auto-orientation based on: If a reference point (e.g., ROI centroid) is provided, orient toward it For 3+ paths: find the tighter endpoint cluster as the root For 2 paths: find the closest endpoint pair as the root

SUM - Enum constant in enum class sc.fiji.snt.analysis.ProfileProcessor.Metric

SUM - Static variable in class sc.fiji.snt.analysis.ShollAnalyzer

sumEdgeWeights() - Method in class sc.fiji.snt.analysis.graph.AnnotationGraph

Gets the sum of all edge weights.

sumEdgeWeights() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Gets the sum of all edge weights.

sumEdgeWeights(boolean) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph

Gets the sum of all edge weights.

summarize() - Method in class sc.fiji.snt.analysis.SNTTable

summarize(boolean) - Method in class sc.fiji.snt.analysis.TreeStatistics

Outputs a summary of the current analysis to the measurements table using the default Tree label.

summarize(String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollTable

Summarizes Profile and ShollStats metrics to a new row.

summarize(String, boolean) - Method in class sc.fiji.snt.analysis.TreeStatistics

Outputs a summary of the current analysis to the measurements table.

summarize(Supplier<SNTTable>, JTable) - Static method in class sc.fiji.snt.gui.GuiUtils.MenuItems

summarize(ShollTable, String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollTable

Runs ShollTable.summarize(String) and appends (copies) the summary row to the specified table

SummarizeSkeleton - Class in sc.fiji.snt.plugin.ij1

This class implements the Summarize Skeleton command.

SummarizeSkeleton() - Constructor for class sc.fiji.snt.plugin.ij1.SummarizeSkeleton

SUN - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

SupplierUtil - Class in sc.fiji.snt.tracing.image

Static utilities for creation of Suppliers of SearchImages

SupplierUtil.ArraySearchImageSupplier<V> - Class in sc.fiji.snt.tracing.image

SupplierUtil.ListSearchImageSupplier<V> - Class in sc.fiji.snt.tracing.image

SupplierUtil.MapSearchImageSupplier<V> - Class in sc.fiji.snt.tracing.image

supportedMetrics() - Static method in class sc.fiji.snt.analysis.ConvexHullAnalyzer

Gets the list of metrics supported by ConvexHullAnalyzer.

supportedMetrics() - Static method in class sc.fiji.snt.analysis.RootAngleAnalyzer

supportedVersion() - Static method in class sc.fiji.snt.io.NDFImporter

SURFACE - Static variable in interface sc.fiji.snt.analysis.sholl.math.ShollStats

Flag for surface normalization (Semi-log/Log-log method)

SURFACE - Static variable in class sc.fiji.snt.viewer.Annotation3D

SURFACE_AND_VOLUME - Static variable in class sc.fiji.snt.viewer.Annotation3D

SURFACE_AREA - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying Surface area statistics.

swapAxes(int, int) - Method in class sc.fiji.snt.Tree

Swaps the coordinates of two axes in this Tree.

swapAxes(ImgPlus<T>, AxisType, AxisType) - Static method in class sc.fiji.snt.util.ImgUtils

Returns a new ImgPlus with two axes swapped.

SWC_APICAL_DENDRITE - Static variable in class sc.fiji.snt.Path

SWC type flag specifying "apical dendrite"

SWC_APICAL_DENDRITE_LABEL - Static variable in class sc.fiji.snt.Path

String representation of Path.SWC_APICAL_DENDRITE

SWC_AXON - Static variable in class sc.fiji.snt.Path

SWC type flag specifying "axon"

SWC_AXON_LABEL - Static variable in class sc.fiji.snt.Path

String representation of Path.SWC_AXON

SWC_CUSTOM - Static variable in class sc.fiji.snt.Path

SWC type flag specifying "custom"

SWC_CUSTOM_LABEL - Static variable in class sc.fiji.snt.Path

String representation of Path.SWC_CUSTOM

SWC_CUSTOM2 - Static variable in class sc.fiji.snt.Path

SWC type flag specifying "custom (2)"

SWC_CUSTOM2_LABEL - Static variable in class sc.fiji.snt.Path

String representation of Path.SWC_CUSTOM2

SWC_DENDRITE - Static variable in class sc.fiji.snt.Path

SWC type flag specifying "(basal) dendrite"

SWC_DENDRITE_LABEL - Static variable in class sc.fiji.snt.Path

String representation of Path.SWC_DENDRITE

SWC_END_POINT - Static variable in class sc.fiji.snt.Path

Deprecated.

SWC_FORK_POINT - Static variable in class sc.fiji.snt.Path

Deprecated.

SWC_GLIA_PROCESS - Static variable in class sc.fiji.snt.Path

SWC type flag specifying "glia process"

SWC_GLIA_PROCESS_LABEL - Static variable in class sc.fiji.snt.Path

String representation of Path.SWC_GLIA_PROCESS

SWC_SOMA - Static variable in class sc.fiji.snt.Path

SWC type flag specifying "soma"

SWC_SOMA_LABEL - Static variable in class sc.fiji.snt.Path

String representation of Path.SWC_SOMA

SWC_TYPE_IGNORED - Static variable in class sc.fiji.snt.util.SNTColor

SWC_UNDEFINED - Static variable in class sc.fiji.snt.Path

SWC type flag specifying "undefined"

SWC_UNDEFINED_LABEL - Static variable in class sc.fiji.snt.Path

String representation of Path.SWC_UNDEFINED

SWC_UNSPECIFIED - Static variable in class sc.fiji.snt.Path

SWC type flag specifying "unspecified neurite"

SWC_UNSPECIFIED_LABEL - Static variable in class sc.fiji.snt.Path

String representation of Path.SWC_UNSPECIFIED

SWCExportDialog - Class in sc.fiji.snt.gui

Implements a dialog for exporting SWC files.

SWCExportDialog(SNTUI, ImagePlus, File) - Constructor for class sc.fiji.snt.gui.SWCExportDialog

SWCExportDialog(SNTUI, ImagePlus, File, boolean) - Constructor for class sc.fiji.snt.gui.SWCExportDialog

SWCExportException - Exception Class in sc.fiji.snt.io

Exception thrown when an error occurs during SWC file export operations.

SWCExportException(String) - Constructor for exception class sc.fiji.snt.io.SWCExportException

SWCImportDialog - Class in sc.fiji.snt.gui

Implements a dialog for importing SWC files.

SWCImportDialog(SNTUI, File) - Constructor for class sc.fiji.snt.gui.SWCImportDialog

SWCPoint - Class in sc.fiji.snt.util

Defines a node in an SWC reconstruction.

SWCPoint(int, int, double, double, double, double, int) - Constructor for class sc.fiji.snt.util.SWCPoint

SWCTypeFilterCmd - Class in sc.fiji.snt.gui.cmds

Implements PathManagerUI's SWC-type filtering Command.

SWCTypeFilterCmd() - Constructor for class sc.fiji.snt.gui.cmds.SWCTypeFilterCmd

SWCTypeOptionsCmd - Class in sc.fiji.snt.gui.cmds

Implements PathManagerUI's SWC-SWC-type tagging Options Command.

SWCTypeOptionsCmd() - Constructor for class sc.fiji.snt.gui.cmds.SWCTypeOptionsCmd

SWCWeightedEdge - Class in sc.fiji.snt.analysis.graph

An extremely simple implementation of a weighted edge for Tree:Directed Graph conversions.

SWCWeightedEdge() - Constructor for class sc.fiji.snt.analysis.graph.SWCWeightedEdge

swellingFactor(double) - Method in class sc.fiji.snt.analysis.detection.AlongPathDetector.Config

Sets AlongPathDetector.Config.swellingFactor.

SwingSafeResult - Class in sc.fiji.snt.gui

Utility class that ensures EDT execution.

SwingSafeResult() - Constructor for class sc.fiji.snt.gui.SwingSafeResult

symDifference(AnnotationGraph, AnnotationGraph) - Static method in class sc.fiji.snt.analysis.graph.AnnotationGraphUtils

Return the graph representing the symmetric difference of the edge sets of graph1 and graph2

SYNC - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

syncCanvasOffset(Path, Path) - Static method in class sc.fiji.snt.util.TreeUtils

Applies the parent's canvas offset to the child path and all its descendants.

syncOverlays() - Method in class sc.fiji.snt.viewer.Bvv

Updates the viewer display to reflect changes in rendered trees and paths.

syncPathManagerList() - Method in class sc.fiji.snt.SciViewSNT

(Re)loads the current list of Paths in the Path Manager list.

syncPathManagerList() - Method in class sc.fiji.snt.viewer.Bvv

Synchronizes the Path Manager contents with BVV display.

syncPathManagerList() - Method in class sc.fiji.snt.viewer.Viewer3D

(Re)loads the current list of Paths in the Path Manager list.

syncSpatialSettingsWithPlugin() - Method in class sc.fiji.snt.PathAndFillManager

syncTransforms() - Method in class sc.fiji.snt.viewer.BvvMultiSource

Forces a repaint.

T

tabbedPaneIcon(JTabbedPane, IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory

table - Variable in class sc.fiji.snt.analysis.TreeStatistics

TABLE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

TABLE_COLUMNS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

TABLE_TITLE - Static variable in class sc.fiji.snt.PathManagerUI

tableWithPlaceholder(TableModel, Supplier<String>, Supplier<String>) - Static method in class sc.fiji.snt.gui.GuiUtils.JTables

Returns a JTable subclass that draws centered placeholder text when the table model is empty.

TabularParser - Class in sc.fiji.snt.analysis.sholl.parsers

A Parser for extracting Sholl profiles from tabular data.

TabularParser(ResultsTable, String, String, int, int) - Constructor for class sc.fiji.snt.analysis.sholl.parsers.TabularParser

Constructs a TabularParser from an ImageJ1 ResultsTable with row range specification.

TabularParser(File, String, String) - Constructor for class sc.fiji.snt.analysis.sholl.parsers.TabularParser

Constructs a TabularParser from a table file.

TabularParser(String, String, String) - Constructor for class sc.fiji.snt.analysis.sholl.parsers.TabularParser

Constructs a TabularParser from a table file path.

TabularParser(ResultsTable, String, String) - Constructor for class sc.fiji.snt.analysis.sholl.parsers.TabularParser

Constructs a TabularParser from an ImageJ2 ResultsTable.

TabularParser(DoubleTable, String, String) - Constructor for class sc.fiji.snt.analysis.sholl.parsers.TabularParser

Constructs a TabularParser from a DoubleTable.

TAG - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

TAG_FILENAME - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Tags/filename

TAG_REGEX_PATTERN - Static variable in class sc.fiji.snt.analysis.growth.GrowthAnalyzer

TAG_REGEX_PATTERN - Static variable in class sc.fiji.snt.plugin.PathMatcherCmd

TAG_REGEX_PATTERN_LEGACY - Static variable in class sc.fiji.snt.plugin.PathMatcherCmd

TAG_UNSET - Static variable in class sc.fiji.snt.seed.SeedPoint

Empty-string sentinel for unset SeedPoint.type / SeedPoint.source.

TAPE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

targetBallName - Static variable in class sc.fiji.snt.SNT

tempMsg(String) - Method in class sc.fiji.snt.gui.GuiUtils

tempMsg(String, int) - Method in class sc.fiji.snt.gui.GuiUtils

temporaryPath - Variable in class sc.fiji.snt.SNT

TERMINAL_EXTENSION_ANGLE - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Terminal branches: Extension angle"

TERMINAL_EXTENSION_ANGLE_REL - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Terminal branches: Extension angle (Rel.)"

TERMINAL_EXTENSION_ANGLE_XY - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Terminal branches: Extension angle XY"

TERMINAL_EXTENSION_ANGLE_XZ - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Terminal branches: Extension angle XZ"

TERMINAL_EXTENSION_ANGLE_ZY - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Terminal branches: Extension angle ZY"

TERMINAL_LENGTH - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics

Flag for "Length of terminal branches (sum)" analysis.

TERMINAL_LENGTH - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Terminal branches: Length"

terminalBranches - Variable in class sc.fiji.snt.analysis.TreeStatistics

TerminalBranchLength() - Constructor for class sc.fiji.snt.analysis.curation.PlausibilityCheck.TerminalBranchLength

terminate() - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

terminate() - Method in interface sc.fiji.snt.analysis.sholl.parsers.Parser

Terminates the parsing operation.

terminate() - Method in class sc.fiji.snt.analysis.sholl.parsers.TabularParser

terminate() - Method in class sc.fiji.snt.analysis.sholl.parsers.TreeParser

TEXT - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

thetaMinDeg(double) - Method in class sc.fiji.snt.util.CrossoverFinder.Config

Sets CrossoverFinder.Config.thetaMinDeg.

THICK_LINE - Static variable in class sc.fiji.snt.analysis.sholl.gui.ShollPlot

Flag for plotting points with a thicker solid line

threadStatus(SearchInterface, int) - Method in class sc.fiji.snt.FillManagerUI

threadStatus(SearchInterface, int) - Method in interface sc.fiji.snt.SearchProgressCallback

threadStatus(SearchInterface, int) - Method in class sc.fiji.snt.SNT

threshold - Variable in class sc.fiji.snt.gui.cmds.AnnotationGraphGeneratorCmd

threshold - Variable in class sc.fiji.snt.gui.cmds.NewGraphOptionsCmd

threshold() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCheck.Warning

Returns the value of the threshold record component.

threshold() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Returns the value of the threshold record component.

tile(Collection<SNTChart>) - Static method in class sc.fiji.snt.analysis.SNTChart

Tiles specified charts displaying them on a grid.

tile(List<? extends Window>) - Static method in class sc.fiji.snt.gui.GuiUtils

tileAll() - Static method in class sc.fiji.snt.analysis.SNTChart

Tiles all open charts displaying them on a grid.

TIMED_OUT - Static variable in class sc.fiji.snt.tracing.SearchThread

timeIndex() - Method in record class sc.fiji.snt.util.ImgUtils.SliceResult

Returns the value of the timeIndex record component.

timeoutSeconds - Variable in class sc.fiji.snt.tracing.AbstractSearch

TimePoint(int, double, Path) - Constructor for record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.TimePoint

Creates an instance of a TimePoint record class.

TIMES - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

TIMESTAMP_REGEX - Static variable in class sc.fiji.snt.SNTUtils

timeStampButton(ActionListener) - Method in class sc.fiji.snt.gui.SNTEditorPane

TIP - Enum constant in enum class sc.fiji.snt.tracing.auto.AutoTracer.SeedRole

Target / endpoint: trace toward this point.

tips - Variable in class sc.fiji.snt.analysis.TreeStatistics

TIPS - Static variable in class sc.fiji.snt.analysis.graph.AnnotationGraph

toBoundingBox3d() - Method in class sc.fiji.snt.util.BoundingBox

toDataset(ImagePlus) - Static method in class sc.fiji.snt.util.ImpUtils

toggle() - Method in class sc.fiji.snt.gui.GuiUtils.JTables.DetachableTable

Convenience: GuiUtils.JTables.DetachableTable.dock() when detached, GuiUtils.JTables.DetachableTable.detach() otherwise.

toggleBvvPanel() - Method in class sc.fiji.snt.BookmarkManager

Shows or hides the floating BVV marker panel.

toggleChannelAndFrameChoice() - Method in class sc.fiji.snt.SNTUI

togglePartsChoice() - Method in class sc.fiji.snt.SNTUI

togglePathsChoice() - Method in class sc.fiji.snt.SNTUI

toggleSecondaryLayerTracing() - Method in class sc.fiji.snt.SNTUI

toggleSnapCursor() - Method in class sc.fiji.snt.SNT

toggleTheme() - Method in class sc.fiji.snt.gui.SNTEditorPane

toggleVisibility() - Static method in class sc.fiji.snt.gui.cmds.ShortcutWindowCmd

toggleVisibility() - Method in class sc.fiji.snt.gui.SNTCommandFinder

Toggles the visibility of the command finder window.

TOILET - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

toImagePlus(ImgPlus<T>) - Static method in class sc.fiji.snt.util.ImgUtils

Convert an ImgPlus to an ImageJ1 ImagePlus.

toImagePlus(ImgPlus<T>, long[], long[]) - Static method in class sc.fiji.snt.util.ImgUtils

Convert an ImgPlus to an ImagePlus, cropping to a bounding box.

toImagePlus(ImgPlus<T>, long[], long[], long, boolean) - Static method in class sc.fiji.snt.util.ImgUtils

Convert an ImgPlus to an ImagePlus, cropping to a bounding box.

toImagePlus(ImgPlus<T>, String) - Static method in class sc.fiji.snt.util.ImgUtils

Convert an ImgPlus to an ImageJ1 ImagePlus.

toImgPlus(ImagePlus) - Static method in class sc.fiji.snt.util.ImpUtils

Convert an ImagePlus to an ImgPlus with calibration and origin metadata.

toImgPlus3D(ImagePlus, int, int) - Static method in class sc.fiji.snt.util.ImpUtils

Convert an ImagePlus to a 3D (XYZ) ImgPlus, extracting a single channel/frame if needed.

TOOL - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

toolbar - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor

toolbarButton(String) - Static method in class sc.fiji.snt.gui.GuiUtils.Buttons

toolbarButton(Action, String) - Static method in class sc.fiji.snt.gui.GuiUtils.Buttons

toolbarButton(IconFactory.GLYPH, Color, float) - Static method in class sc.fiji.snt.gui.GuiUtils.Buttons

toolbarToggleButton(Action, String, IconFactory.GLYPH, IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.GuiUtils.Buttons

toOverlay(Overlay) - Method in class sc.fiji.snt.BookmarkManager

Adds the bookmark ROIs to the specified overlay.

TOP - Enum constant in enum class sc.fiji.snt.viewer.Viewer3D.ViewMode

Deprecated.

Use XY instead

toPath(double[]) - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Creates a single-node Path representing the soma.

topKByConfidence(int) - Method in class sc.fiji.snt.seed.SeedOverlay

Returns up to k seeds from the visible range ([lowConfidence, highConfidence]) with the highest confidence.

toPointInImage() - Method in class sc.fiji.snt.seed.SeedPoint

Returns a PointInImage carrying this seed's coordinates and radius, useful when handing the seed to APIs that expect the concrete point class rather than the SNTPoint interface.

toPointRoi(List<Detection>, ImagePlus, String, Color) - Static method in class sc.fiji.snt.analysis.RoiConverter

Creates a grouped PointRoi from a list of Detections.

toRoi(String) - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Creates an ImageJ ROI of the specified type.

toRoiAtDetectedZ(String) - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Creates an ImageJ ROI using the stored Z-slice position.

toRoiManager() - Method in class sc.fiji.snt.BookmarkManager

Adds the bookmarks to the ROI Manager.

toRois(Collection<SeedPoint>, ImagePlus) - Static method in class sc.fiji.snt.seed.SeedRois

Converts the given seeds to ROIs.

TortuosityConsistency() - Constructor for class sc.fiji.snt.analysis.curation.PlausibilityCheck.TortuosityConsistency

toSeeds(Roi[], ImagePlus, double, String, String) - Static method in class sc.fiji.snt.seed.SeedRois

Converts the given ROIs to seeds.

toSNTPoint() - Method in class sc.fiji.snt.analysis.detection.Detection

Returns this detection as an SNTPoint.

toStack(Collection<ImagePlus>) - Static method in class sc.fiji.snt.util.ImpUtils

toString() - Method in record class sc.fiji.snt.analysis.CircularModels.VonMisesFit

Returns a string representation of this record class.

toString() - Method in record class sc.fiji.snt.analysis.curation.CurationTags.Partition

Returns a string representation of this record class.

toString() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCalibrator.CheckSummary

Returns a string representation of this record class.

toString() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCheck.Warning

Returns a string representation of this record class.

toString() - Method in class sc.fiji.snt.analysis.detection.AlongPathDetector.Config

toString() - Method in class sc.fiji.snt.analysis.detection.Detection

toString() - Method in class sc.fiji.snt.analysis.detection.LabelProximityDetector.Config

toString() - Method in class sc.fiji.snt.analysis.detection.PeripathDetector.Config

toString() - Method in class sc.fiji.snt.analysis.graph.AnnotationWeightedEdge

toString() - Method in class sc.fiji.snt.analysis.graph.SWCWeightedEdge

toString() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalysisResults.GrowthSummaryStatistics

Returns a string representation of this record class.

toString() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.ElongationEvent

Returns a string representation of this record class.

toString() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhase

Returns a string representation of this record class.

toString() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.RetractionEvent

Returns a string representation of this record class.

toString() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.TimePoint

Returns a string representation of this record class.

toString() - Method in class sc.fiji.snt.analysis.growth.NeuriteGrowthData

toString() - Method in record class sc.fiji.snt.analysis.MultiSpectralRefiner.Parameters

Returns a string representation of this record class.

toString() - Method in class sc.fiji.snt.analysis.PCAnalyzer.PrincipalAxis

toString() - Method in enum class sc.fiji.snt.analysis.ProfileProcessor.Metric

toString() - Method in enum class sc.fiji.snt.analysis.ProfileProcessor.Shape

toString() - Method in record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.PolarPeak

Returns a string representation of this record class.

toString() - Method in record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.Report

Creates an adaptive summary tailored to common regimes: No preferred directions when both ADC and ODC are very low or no peaks are found. Single preferred direction when ADC is strong and exactly one robust peak is detected. Preferred orientation (axis) when ODC is strong but ADC is weak. Multiple preferred directions listing up to three top angles otherwise.

toString() - Method in enum class sc.fiji.snt.analysis.sholl.math.ShollStats.DataMode

toString() - Method in class sc.fiji.snt.analysis.sholl.Profile

toString() - Method in class sc.fiji.snt.annotation.AllenCompartment

toString() - Method in class sc.fiji.snt.annotation.DrosophilaCompartment

toString() - Method in class sc.fiji.snt.Fill

toString() - Method in enum class sc.fiji.snt.FillConverter.ResultType

toString() - Method in class sc.fiji.snt.gui.DemoRunner.Demo

toString() - Method in record class sc.fiji.snt.io.OmeAxisUtils.OmeMetadata

Returns a string representation of this record class.

toString() - Method in record class sc.fiji.snt.MultiPathTracerCanvas.Entry

Returns a string representation of this record class.

toString() - Method in class sc.fiji.snt.NearPoint

toString() - Method in class sc.fiji.snt.Path

This toString() method shows details of the path which is actually being displayed, not necessarily this path object.

toString() - Method in class sc.fiji.snt.seed.SeedPoint

toString() - Method in enum class sc.fiji.snt.SNT.CostType

toString() - Method in enum class sc.fiji.snt.SNT.FilterType

toString() - Method in enum class sc.fiji.snt.SNT.HeuristicType

toString() - Method in enum class sc.fiji.snt.SNT.SearchImageType

toString() - Method in enum class sc.fiji.snt.SNT.SearchType

toString() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Returns a string representation of this record class.

toString() - Method in class sc.fiji.snt.tracing.DefaultSearchNode

toString() - Method in class sc.fiji.snt.util.BoundingBox

toString() - Method in class sc.fiji.snt.util.CrossoverFinder.Config

toString() - Method in class sc.fiji.snt.util.CrossoverFinder.CrossoverEvent

toString() - Method in record class sc.fiji.snt.util.ImgUtils.SliceResult

Returns a string representation of this record class.

toString() - Method in class sc.fiji.snt.util.PointInImage

toString() - Method in class sc.fiji.snt.util.ShollPoint

toString() - Method in class sc.fiji.snt.util.SNTColor

toString() - Method in class sc.fiji.snt.util.SWCPoint

toString() - Method in record class sc.fiji.snt.util.TreeUtils.EndpointClusterAnalysis

Returns a string representation of this record class.

toString() - Method in record class sc.fiji.snt.util.TreeUtils.EndpointMatch

Returns a string representation of this record class.

toString() - Method in class sc.fiji.snt.viewer.Bvv.Keyframe

Serializes this keyframe to a single-line string: transform=d0,d1,...,d11|cam=dCam,near,far|visible=a;b;c|accel=N

toString(Iterable<T>) - Static method in class sc.fiji.snt.gui.GuiUtils

toString(GenericTable) - Static method in class sc.fiji.snt.analysis.SNTTable

toString(GenericTable, int, int) - Static method in class sc.fiji.snt.analysis.SNTTable

toTable() - Method in class sc.fiji.snt.analysis.curation.PlausibilityCalibrator.CalibrationResult

Returns a human-readable summary table of the calibration results.

total() - Method in record class sc.fiji.snt.analysis.curation.CurationTags.Partition

Total path count across all four buckets.

totalElongations() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalysisResults.GrowthSummaryStatistics

Returns the value of the totalElongations record component.

totalRetractions() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalysisResults.GrowthSummaryStatistics

Returns the value of the totalRetractions record component.

toUnsignedShortIfFloat(RandomAccessibleInterval<T>) - Static method in class sc.fiji.snt.util.ImgUtils

Returns a 16-bit view of the given RAI if its pixel type is FloatType, normalizing values to the full 16-bit range using the data's actual min/max.

toUnsignedShortIfFloat(RandomAccessibleInterval<T>, double, double) - Static method in class sc.fiji.snt.util.ImgUtils

Returns a 16-bit view of the given RAI if its pixel type is FloatType, normalizing to the given min/max range.

trace() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Traces the neuron and returns a Tree.

trace() - Method in interface sc.fiji.snt.tracing.auto.AutoTracer

Traces the neuronal structure and returns a single merged Tree.

traceMultiSoma(List<SomaUtils.SomaResult>) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Traces multiple somas in a single image using a NeuTube-style recovery pass strategy.

TracerCanvas - Class in sc.fiji.snt

Provides rendering capabilities for visualizing paths, overlays, and additional interactive elements in an ImageJ canvas.

TracerThread - Class in sc.fiji.snt.tracing

SNT's default tracer thread: explores between two points in an image, doing an A* search with a choice of distance measures.

TracerThread(Dataset, int, int, int, int, int, int, int, long, SNT.SearchImageType, Cost, Heuristic) - Constructor for class sc.fiji.snt.tracing.TracerThread

TracerThread(Dataset, int, int, int, int, int, int, int, long, Cost, Heuristic) - Constructor for class sc.fiji.snt.tracing.TracerThread

TracerThread(Dataset, int, int, int, int, int, int, Cost) - Constructor for class sc.fiji.snt.tracing.TracerThread

TracerThread(Dataset, int, int, int, int, int, int, Cost, Heuristic) - Constructor for class sc.fiji.snt.tracing.TracerThread

TracerThread(RandomAccessibleInterval<? extends RealType<?>>, Calibration, int, int, int, int, int, int, int, long, SNT.SearchImageType, Cost, Heuristic) - Constructor for class sc.fiji.snt.tracing.TracerThread

TracerThread(SNT, int, int, int, int, int, int) - Constructor for class sc.fiji.snt.tracing.TracerThread

TracerThread(SNT, int, int, int, int, int, int, Cost, Heuristic) - Constructor for class sc.fiji.snt.tracing.TracerThread

TracerThread(SNT, RandomAccessibleInterval<? extends RealType<?>>, int, int, int, int, int, int, Cost, Heuristic) - Constructor for class sc.fiji.snt.tracing.TracerThread

TRACES_FILE_TYPE_COMPRESSED_XML - Static variable in class sc.fiji.snt.PathAndFillManager

TRACES_FILE_TYPE_ML_JSON - Static variable in class sc.fiji.snt.PathAndFillManager

TRACES_FILE_TYPE_NDF - Static variable in class sc.fiji.snt.PathAndFillManager

TRACES_FILE_TYPE_NEUROLUCIDA - Static variable in class sc.fiji.snt.PathAndFillManager

TRACES_FILE_TYPE_SWC - Static variable in class sc.fiji.snt.PathAndFillManager

TRACES_FILE_TYPE_UNCOMPRESSED_XML - Static variable in class sc.fiji.snt.PathAndFillManager

TracesFileFormatException - Exception Class in sc.fiji.snt.io

Exception thrown when an error occurs while parsing or validating traces file formats.

TracesFileFormatException(String) - Constructor for exception class sc.fiji.snt.io.TracesFileFormatException

traceToGraph() - Method in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

Traces the structure and returns a DirectedWeightedGraph.

traceToGraph() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

traceTrees() - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Traces the neuron and returns a list of Trees.

traceTrees() - Method in interface sc.fiji.snt.tracing.auto.AutoTracer

Traces the neuronal structure and returns a list of Trees.

traceTrees() - Method in class sc.fiji.snt.tracing.auto.BinaryTracer

TRACING_PAUSED - Static variable in class sc.fiji.snt.SNTUI

Flag specifying tracing functions are (currently) disabled.

tracingHalted - Variable in class sc.fiji.snt.SNT

transferAnnotationIdsToNodeValues(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils

Transfers brain annotation IDs to node values for all paths in a Tree.

transform - Variable in class sc.fiji.snt.viewer.Bvv.Keyframe

Viewer transform (camera position + zoom + rotation).

transform(String) - Method in class sc.fiji.snt.Tree

Transforms this tree in place using standardized flags.

transform(Collection<Tree>, String, boolean) - Static method in class sc.fiji.snt.Tree

Transforms a collection of trees using standardized flags.

transform(PathTransformer) - Method in class sc.fiji.snt.util.PointInImage

transform(PathTransformer, ImagePlus, ImagePlus) - Method in class sc.fiji.snt.Path

transformationFinished(View) - Method in class sc.fiji.snt.PathAndFillManager

transformationStarted(View) - Method in class sc.fiji.snt.PathAndFillManager

transformationUpdated(View) - Method in class sc.fiji.snt.PathAndFillManager

transformedCopy(String) - Method in class sc.fiji.snt.Tree

Retrieves a transformed duplicate of this tree.

transformPaths(PathTransformer, ImagePlus, ImagePlus) - Method in class sc.fiji.snt.PathAndFillManager

transformPoint(double, double, double, double[]) - Method in interface sc.fiji.snt.PathTransformer

transformPoint(double, double, double, int[]) - Method in interface sc.fiji.snt.PathTransformer

transformPoint(int, int, int, double[]) - Method in interface sc.fiji.snt.PathTransformer

transformPoint(int, int, int, int[]) - Method in interface sc.fiji.snt.PathTransformer

translate(double, double, double) - Method in class sc.fiji.snt.Tree

Translates the tree by the specified offset.

translate(Collection<String>, SNTPoint) - Method in class sc.fiji.snt.viewer.Viewer3D

Translates the specified collection of Trees.

translate(Tree, SNTPoint) - Method in class sc.fiji.snt.viewer.Viewer3D

Translates the specified Tree.

translate(SNTPoint) - Method in class sc.fiji.snt.viewer.OBJMesh

Translates the vertices of this mesh by the specified offset.

TranslateReconstructionsCmd - Class in sc.fiji.snt.gui.cmds

Implements Reconstruction Viewer's 'Translate...' command.

TranslateReconstructionsCmd() - Constructor for class sc.fiji.snt.gui.cmds.TranslateReconstructionsCmd

TRASH - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

tree - Variable in class sc.fiji.snt.analysis.TreeStatistics

Tree - Class in sc.fiji.snt

Utility class to access a Collection of Paths (typically a complete reconstruction).

Tree() - Constructor for class sc.fiji.snt.Tree

Instantiates a new empty Tree.

Tree(String) - Constructor for class sc.fiji.snt.Tree

Instantiates a new tree from a SWC, TRACES or JSON file.

Tree(String, int...) - Constructor for class sc.fiji.snt.Tree

Instantiates a new tree from a filtered SWC, TRACES or JSON file.

Tree(String, String) - Constructor for class sc.fiji.snt.Tree

Instantiates a new tree from a SWC, TRACES or JSON file with filtering.

Tree(Collection<Path>) - Constructor for class sc.fiji.snt.Tree

Instantiates a new Tree from a set of paths.

Tree(Collection<SWCPoint>, String) - Constructor for class sc.fiji.snt.Tree

Instantiates a Tree from a collection of reconstruction nodes.

Tree(DirectedWeightedGraph, String) - Constructor for class sc.fiji.snt.Tree

Instantiates a new Tree from a DirectedWeightedGraph with the specified label.

Tree(DirectedWeightedGraph, String, boolean) - Constructor for class sc.fiji.snt.Tree

Instantiates a new Tree from a DirectedWeightedGraph with control over path structure preservation.

TREE - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

TreeAnalyzer - Class in sc.fiji.snt.analysis

Deprecated.

Use TreeStatistics instead

TreeAnalyzer(Tree) - Constructor for class sc.fiji.snt.analysis.TreeAnalyzer

Deprecated.

Use TreeStatistics constructors instead

TreeColorMapper - Class in sc.fiji.snt.analysis

Class for color coding Trees.

TreeColorMapper() - Constructor for class sc.fiji.snt.analysis.TreeColorMapper

Instantiates the mapper.

TreeColorMapper(Context) - Constructor for class sc.fiji.snt.analysis.TreeColorMapper

Instantiates the mapper.

TreeGraphAdapter - Class in sc.fiji.snt.viewer.geditor

JGraphX adapter for visualizing tree graphs as SWC morphologies.

TreeGraphAdapter(DirectedWeightedGraph) - Constructor for class sc.fiji.snt.viewer.geditor.TreeGraphAdapter

TreeGraphAdapter(DirectedWeightedGraph, String) - Constructor for class sc.fiji.snt.viewer.geditor.TreeGraphAdapter

TreeGraphComponent - Class in sc.fiji.snt.viewer.geditor

JGraphX visualization component for tree graphs representing neurite morphologies.

TreeGraphComponent(TreeGraphAdapter, Context) - Constructor for class sc.fiji.snt.viewer.geditor.TreeGraphComponent

TreeGraphRecViewerCmd - Class in sc.fiji.snt.gui.cmds

SciJava Command for displaying tree graph structures in the Reconstruction Viewer as interactive 3D visualizations.

TreeGraphRecViewerCmd() - Constructor for class sc.fiji.snt.gui.cmds.TreeGraphRecViewerCmd

TreeMapperCmd - Class in sc.fiji.snt.plugin

Command for color coding trees according to their properties and statistics, using MultiTreeColorMapper and TreeColorMapper.

TreeMapperCmd() - Constructor for class sc.fiji.snt.plugin.TreeMapperCmd

TreeParser - Class in sc.fiji.snt.analysis.sholl.parsers

A Parser for extracting Sholl Profiles from a Tree.

TreeParser(Tree) - Constructor for class sc.fiji.snt.analysis.sholl.parsers.TreeParser

Instantiates a new Tree Parser.

TreeProperties - Interface in sc.fiji.snt

Allows standardized metadata to be associated to a Tree.

TreeStatistics - Class in sc.fiji.snt.analysis

Computes summary and descriptive statistics from properties of Paths and Nodes in a Tree, including convenience methods to plot distributions of such data.

TreeStatistics(Collection<Path>, String) - Constructor for class sc.fiji.snt.analysis.TreeStatistics

Instantiates Tree statistics from a collection of paths.

TreeStatistics(Tree) - Constructor for class sc.fiji.snt.analysis.TreeStatistics

Instantiates a new instance from a collection of Paths

TreeToRaster - Class in sc.fiji.snt.util

Rasterizes a Tree into a 3D image using frustum (truncated-cone) geometry with partial-volume supersampling.

TreeToRaster(Tree) - Constructor for class sc.fiji.snt.util.TreeToRaster

Constructs a new rasterizer for the given tree.

TreeUtils - Class in sc.fiji.snt.util

Static utilities for Trees.

TreeUtils.EndpointClusterAnalysis - Record Class in sc.fiji.snt.util

Result of analyzing which endpoint cluster (starts vs ends) is tighter.

TreeUtils.EndpointMatch - Record Class in sc.fiji.snt.util

Result of finding the closest endpoints between two paths.

TRIAL - Static variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Fast Marching state: voxel is in the narrow-band trial set.

triggerZoomEvent(boolean, int, int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

trimNaNCounts() - Method in class sc.fiji.snt.analysis.sholl.Profile

trimZeroCounts() - Method in class sc.fiji.snt.analysis.sholl.Profile

truncate(String, int) - Static method in class sc.fiji.snt.gui.GuiUtils

tryReallyHardToGuessMetric(String) - Static method in class sc.fiji.snt.analysis.TreeStatistics

tTest(String, String, String) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics

Computes a two-sample, two-tailed t-test P-value for two of groups being analyzed.

Tubeness<T,U> - Class in sc.fiji.snt.filter

Computes a tubeness (vesselness) filter on a multi-dimensional image using multi-scale eigenvalue analysis of the Hessian matrix.

Tubeness() - Constructor for class sc.fiji.snt.filter.Tubeness

Empty constructor required for proper loading by OpService.

Tubeness(double[], double[]) - Constructor for class sc.fiji.snt.filter.Tubeness

Constructs a Tubeness filter with the specified scales and spacing.

Tubeness(double[], double[], int) - Constructor for class sc.fiji.snt.filter.Tubeness

Constructs a Tubeness filter with the specified scales, spacing, and number of threads.

TUBENESS - Enum constant in enum class sc.fiji.snt.SNT.FilterType

tubularGeodesicsThread - Variable in class sc.fiji.snt.SNT

TubularGeodesicsTracer - Class in sc.fiji.snt.tracing

A tracer thread for FijiITKInterface.TubularGeodesics (assumes the tubularity add-on to be installed)

TubularGeodesicsTracer(File, float, float, float, float, float, float, double, double, double, String) - Constructor for class sc.fiji.snt.tracing.TubularGeodesicsTracer

tubularGeodesicsTracingEnabled - Variable in class sc.fiji.snt.SNT

tuneBranches(DirectedWeightedGraph, double) - Method in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

Tunes branch-point topology by re-parenting nodes adjacent to bifurcations.

TwoDHistCmd - Class in sc.fiji.snt.gui.cmds

Command for plotting 2D histograms of morphometric distributions

TwoDHistCmd() - Constructor for class sc.fiji.snt.gui.cmds.TwoDHistCmd

TWSLoaderCmd - Class in sc.fiji.snt.plugin

Command for sending Path-converted ROIs to a new TWS instance.

TWSLoaderCmd() - Constructor for class sc.fiji.snt.plugin.TWSLoaderCmd

type - Variable in class sc.fiji.snt.event.SNTEvent

type - Variable in class sc.fiji.snt.seed.SeedPoint

Free-form semantic label (e.g.

type - Variable in class sc.fiji.snt.util.SWCPoint

The SWC-type flag of this node (Path.SWC_SOMA, Path.SWC_DENDRITE, etc.)

type() - Method in record class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhase

Returns the value of the type record component.

type() - Method in class sc.fiji.snt.util.SNTColor

Retrieves the SWC type

TYPE - Enum constant in enum class sc.fiji.snt.seed.SeedOverlay.ColorMode

U

ui - Variable in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

ui - Variable in class sc.fiji.snt.SNT

uiFontSize() - Static method in class sc.fiji.snt.gui.GuiUtils

uiReadyForModeChange() - Method in class sc.fiji.snt.SNT

uiScale() - Static method in class sc.fiji.snt.gui.GuiUtils

Returns the effective UI scale factor for the current display environment, accounting for HiDPI displays and user-configured scaling.

uiService - Variable in class sc.fiji.snt.gui.cmds.CommonDynamicCmd

UnaryComputerOpCellLoader<T,S,R> - Class in sc.fiji.snt.filter

This class is taken directly from https://github.com/saalfeldlab/hot-knife

UnaryComputerOpCellLoader(R, OpService, Class<? extends Op>, Object[]) - Constructor for class sc.fiji.snt.filter.UnaryComputerOpCellLoader

UnaryComputerOpCellLoader(R, UnaryComputerOp<R, RandomAccessibleInterval<S>>) - Constructor for class sc.fiji.snt.filter.UnaryComputerOpCellLoader

Constructs a new UnaryComputerOpCellLoader with the specified source and operation.

UNASSIGNED_VALUE - Static variable in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

UNASSIGNED_VALUE - Static variable in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

undo() - Static method in class sc.fiji.snt.gui.GuiUtils.Buttons

undo(Action) - Static method in class sc.fiji.snt.gui.GuiUtils.Buttons

UNDO - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

undoHandler - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor

undoLastSegment() - Method in class sc.fiji.snt.SNT

undoManager - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor

unfreeze() - Method in class sc.fiji.snt.viewer.Viewer3D

Allows scene to be interactive.

union(Collection<AnnotationGraph>) - Static method in class sc.fiji.snt.analysis.graph.AnnotationGraphUtils

Return the graph representing the union of the edge sets of a collection of graphs.

unit - Variable in class sc.fiji.snt.viewer.OBJMesh

UNITS_PHYSICAL - Static variable in class sc.fiji.snt.gui.cmds.ImportSeedPointsCmd

univ - Variable in class sc.fiji.snt.SNT

universeClosed() - Method in class sc.fiji.snt.PathAndFillManager

Deprecated.

UnknownMetricException - Exception Class in sc.fiji.snt.analysis

Exception thrown when a requested metric is not available or recognized.

UnknownMetricException(String) - Constructor for exception class sc.fiji.snt.analysis.UnknownMetricException

UNLINK - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

unMap(Collection<Path>) - Static method in class sc.fiji.snt.analysis.ColorMapper

Removes color mapping from the specified collection of paths.

unMap(Tree) - Static method in class sc.fiji.snt.analysis.ColorMapper

Removes color mapping from all paths in the specified tree.

unreviewed() - Method in record class sc.fiji.snt.analysis.curation.CurationTags.Partition

Returns the value of the unreviewed record component.

unsavedPaths - Variable in class sc.fiji.snt.PathAndFillManager

unscaledOrigin() - Method in class sc.fiji.snt.util.BoundingBox

Retrieves the origin of this box in unscaled ("pixel" units)

unscaledOriginOpposite() - Method in class sc.fiji.snt.util.BoundingBox

Retrieves the origin opposite of this box in unscaled ("pixel" units)

UNSET - Static variable in interface sc.fiji.snt.analysis.sholl.ProfileProperties

UNSET - Static variable in interface sc.fiji.snt.TreeProperties

unsetStartJoin() - Method in class sc.fiji.snt.Path

Deprecated.

unsure() - Method in record class sc.fiji.snt.analysis.curation.CurationTags.Partition

Returns the value of the unsure record component.

UNSURE - Static variable in class sc.fiji.snt.analysis.curation.CurationTags

Tag value applied to paths flagged for follow-up review.

unzoomAllPanes() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

update() - Method in class sc.fiji.snt.PathManagerUI

Refreshes (Repaints) the Path Manager JTree.

update(boolean) - Method in class sc.fiji.snt.PathManagerUI

Refreshes (Repaints) the Path Manager JTree.

update3DViewerContents() - Method in class sc.fiji.snt.PathAndFillManager

updateAllViewers() - Method in class sc.fiji.snt.SNT

updateAndDisplayTable() - Method in class sc.fiji.snt.analysis.TreeStatistics

Updates and displays the measurements table.

updateAndDisplayTable() - Method in class sc.fiji.snt.plugin.PathOrderAnalysisCmd

updateAssignDiameterSpinner() - Method in class sc.fiji.snt.SNTUI

updateBoundingBox() - Method in class sc.fiji.snt.PathAndFillManager

updateColorBarLegend(double, double) - Method in class sc.fiji.snt.viewer.Viewer3D

Updates the existing color bar legend to new properties.

updateCursor(double, double, double) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

updateCursor(double, double, double) - Method in class sc.fiji.snt.SNT

updateDisplay() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay

updateDisplay() - Method in class sc.fiji.snt.analysis.SNTTable

Updates the existing table display.

updateDisplayCanvases() - Method in class sc.fiji.snt.SNT

Rebuilds display canvas(es) to ensure all paths are contained in the image.

updateHyperStackPosition() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCommonCmd

updateImageContent(int) - Method in class sc.fiji.snt.SNT

Deprecated.

updateMip() - Method in class sc.fiji.snt.gui.PaletteOptions

Refreshes the MIP overlay (if currently shown) so it picks up LUT/min/max changes.

updateNonTracingViewers() - Method in class sc.fiji.snt.SNT

updatePosition(double, double, double) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

updateScene() - Method in class sc.fiji.snt.viewer.Bvv.AnnotationOverlay

Ensure renderers/nodes reflect current annotation list.

updateSecLayerWidgets() - Method in class sc.fiji.snt.SNTUI

updateSettingsString() - Method in class sc.fiji.snt.FillManagerUI

updateSettingsString() - Method in class sc.fiji.snt.SNTUI

updateStatus(String, int, int) - Method in class sc.fiji.snt.viewer.Bvv

Updates the progress bar at the bottom of the BVV frame.

updateTable() - Method in class sc.fiji.snt.PathManagerUI

updateThresholdWidget(double) - Method in class sc.fiji.snt.FillManagerUI

updateTitle() - Method in class sc.fiji.snt.viewer.geditor.GraphEditor

updateTracingViewers(boolean) - Method in class sc.fiji.snt.SNT

updateUI() - Method in class sc.fiji.snt.gui.SNTEditorPane

updateVertexProperties() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Re-assigns a unique Integer identifier to each vertex based on visit order during Depth First Search.

updateView() - Method in class sc.fiji.snt.viewer.Viewer3D

Updates the scene bounds to ensure all visible objects are displayed.

updateViewers() - Method in class sc.fiji.snt.SNTService

Script-friendly method for updating (refreshing) all viewers currently in use by SNT.

UPLOAD - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

upperT - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

upsample(double) - Method in class sc.fiji.snt.Path

Upsamples this path by spacing nodes at a specified distance.

upsample(double) - Method in class sc.fiji.snt.Tree

Downsamples the tree, i.e., increases the density of its nodes by decreasing internode spacing.

URL - Static variable in class sc.fiji.snt.analysis.sholl.ShollUtils

URL - Static variable in class sc.fiji.snt.plugin.ij1.Strahler

Usage Example - Search tag in package sc.fiji.snt.tracing

Section

Usage Example - Search tag in package sc.fiji.snt.tracing.auto

Section

use3DViewer - Variable in class sc.fiji.snt.SNT

USER_DOCTOR - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

useSnapWindow - Variable in class sc.fiji.snt.SNTUI

useStartNodes() - Method in record class sc.fiji.snt.util.TreeUtils.EndpointClusterAnalysis

Returns the value of the useStartNodes record component.

useSWCcolors(boolean) - Method in class sc.fiji.snt.analysis.RoiConverter

Specifies coloring of ROIs by SWC type.

usingNonPhysicalUnits() - Method in class sc.fiji.snt.PathAndFillManager

Utils() - Constructor for class sc.fiji.snt.viewer.Viewer3D.Utils

V

v - Variable in class sc.fiji.snt.util.PointInImage

A property associated with this point (e.g., voxel intensity) (optional field)

validate() - Method in class sc.fiji.snt.analysis.SNTTable

validate() - Method in class sc.fiji.snt.viewer.Viewer3D

Checks if all drawables in the 3D scene are being rendered properly, rebuilding the entire scene if not.

validateBeforeTracing(Roi, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean) - Method in class sc.fiji.snt.plugin.BinaryTracerCommonCmd

Validates configuration before tracing begins.

validateBeforeTracing(Roi, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean) - Method in class sc.fiji.snt.plugin.BinaryTracerFileCmd

validateFit() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

validateFit() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

validFit() - Method in class sc.fiji.snt.analysis.sholl.math.LinearProfileStats

validFit() - Method in class sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

validFit() - Method in class sc.fiji.snt.analysis.sholl.math.PolarProfileStats

validFit() - Method in interface sc.fiji.snt.analysis.sholl.math.ShollStats

validInput() - Method in class sc.fiji.snt.plugin.StrahlerCmd

Assesses if all trees being analyzed can be parsed (A tree won't be parsed, if topologically invalid, e.g., by containing a loop, or disconnected Paths).

validRequirements(boolean) - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCommonCmd

validSoma() - Method in class sc.fiji.snt.Tree

Checks whether this Tree has a valid soma annotation, i.e., only a single primary path tagged with Path.SWC_SOMA.

value() - Method in record class sc.fiji.snt.analysis.curation.PlausibilityCheck.Warning

Returns the value of the value record component.

value() - Method in record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.PolarPeak

Returns the value of the value record component.

valueChanged(TreeSelectionEvent) - Method in class sc.fiji.snt.PathManagerUI

valueOf(String) - Static method in enum class sc.fiji.snt.analysis.CircularModels.Domain

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.analysis.curation.PlausibilityCheck.Severity

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhaseType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.analysis.ProfileProcessor.Metric

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.analysis.ProfileProcessor.Shape

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.analysis.sholl.math.ShollStats.DataMode

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.FillConverter.ResultType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.FillManagerUI.State

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.gui.IconFactory.GLYPH

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.seed.SeedOverlay.ColorMode

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.SNT.CostType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.SNT.FilterType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.SNT.HeuristicType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.SNT.SearchImageType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.SNT.SearchType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.tracing.auto.AbstractGWDTTracer.WaypointBiasSource

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.tracing.auto.AutoTracer.SeedRole

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.tracing.BiSearchNode.State

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in class sc.fiji.snt.util.SNTColor

Parses a color from the given string.

valueOf(String) - Static method in enum class sc.fiji.snt.viewer.Viewer3D.AnimationMode

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.viewer.Viewer3D.RotationAxis

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class sc.fiji.snt.viewer.Viewer3D.ViewMode

Returns the enum constant of this class with the specified name.

values() - Static method in enum class sc.fiji.snt.analysis.CircularModels.Domain

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.analysis.curation.PlausibilityCheck.Severity

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.analysis.growth.GrowthAnalyzer.GrowthPhaseType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.analysis.ProfileProcessor.Metric

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.analysis.ProfileProcessor.Shape

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.analysis.sholl.math.ShollStats.DataMode

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.FillConverter.ResultType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.FillManagerUI.State

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.gui.IconFactory.GLYPH

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.seed.SeedOverlay.ColorMode

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.SNT.CostType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.SNT.FilterType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.SNT.HeuristicType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.SNT.SearchImageType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.SNT.SearchType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.tracing.auto.AbstractGWDTTracer.WaypointBiasSource

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.tracing.auto.AutoTracer.SeedRole

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.tracing.BiSearchNode.State

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.viewer.Viewer3D.AnimationMode

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.viewer.Viewer3D.RotationAxis

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class sc.fiji.snt.viewer.Viewer3D.ViewMode

Returns an array containing the constants of this enum class, in the order they are declared.

VALUES - Static variable in class sc.fiji.snt.analysis.NodeColorMapper

Flag for statistics on node "Node intensity values"

VALUES - Static variable in class sc.fiji.snt.analysis.NodeStatistics

Flag for statistics on "Node intensity values"

VALUES - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Node intensity nodes

VALUES - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag for analysis of Node intensity values, an optional numeric property that can be assigned to Path nodes (e.g., voxel intensities), assigned via PathProfiler.

variance() - Method in record class sc.fiji.snt.util.TreeUtils.EndpointClusterAnalysis

Returns the value of the variance record component.

VARIANCE - Enum constant in enum class sc.fiji.snt.analysis.ProfileProcessor.Metric

verbose - Static variable in class sc.fiji.snt.SNT

verbose - Variable in class sc.fiji.snt.tracing.AbstractSearch

verbose - Variable in class sc.fiji.snt.tracing.auto.AbstractAutoTracer

verbose - Variable in class sc.fiji.snt.tracing.SearchThread

VERSION - Static variable in class sc.fiji.snt.annotation.AllenUtils

VERSION - Static variable in class sc.fiji.snt.SNTUtils

versionInUse() - Method in class sc.fiji.snt.Path

Deprecated.

Use Path.isActiveVersion() instead

vertexSet(char) - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Returns the subset of vertices contained in the given hemisphere

VERTICES - Static variable in class sc.fiji.snt.analysis.graph.GraphColorMapper

VERTICES_AND_EDGES - Static variable in class sc.fiji.snt.analysis.graph.GraphColorMapper

VFBUtils - Class in sc.fiji.snt.annotation

Utility methods for accessing/handling Virtual Fly Brain (VFB) annotations

VIDEO - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

Viewer2D - Class in sc.fiji.snt.viewer

Class for rendering Trees as 2D plots that can be exported as SVG, PNG or PDF.

Viewer2D() - Constructor for class sc.fiji.snt.viewer.Viewer2D

Instantiates an empty 2D viewer using SNT's default context.

Viewer2D(Context) - Constructor for class sc.fiji.snt.viewer.Viewer2D

Instantiates an empty 2D viewer.

Viewer2D(Context, Viewer2D) - Constructor for class sc.fiji.snt.viewer.Viewer2D

Instantiates an empty 2D viewer.

Viewer3D - Class in sc.fiji.snt.viewer

Implements SNT's Reconstruction Viewer.

Viewer3D() - Constructor for class sc.fiji.snt.viewer.Viewer3D

Instantiates Viewer3D without the 'Controls' dialog ('kiosk mode').

Viewer3D(boolean) - Constructor for class sc.fiji.snt.viewer.Viewer3D

Script-friendly constructor.

Viewer3D(boolean, String) - Constructor for class sc.fiji.snt.viewer.Viewer3D

Script-friendly constructor.

Viewer3D(Context) - Constructor for class sc.fiji.snt.viewer.Viewer3D

Instantiates an interactive Viewer3D with GUI Controls to import, manage and customize the Viewer's scene.

Viewer3D(SNT) - Constructor for class sc.fiji.snt.viewer.Viewer3D

Viewer3D.AnimationMode - Enum Class in sc.fiji.snt.viewer

Animation styles for live and recorded rotations.

Viewer3D.ManagerPanel - Class in sc.fiji.snt.viewer

Viewer3D.RotationAxis - Enum Class in sc.fiji.snt.viewer

Axes of rotation for animated sequences and live rotations.

Viewer3D.Utils - Class in sc.fiji.snt.viewer

Viewer3D.ViewMode - Enum Class in sc.fiji.snt.viewer

Presets of a scene's view point.

viewers() - Method in class sc.fiji.snt.viewer.MultiViewer3D

VIRIDIS - Static variable in class sc.fiji.snt.util.ColorMaps

visibleActors - Variable in class sc.fiji.snt.viewer.Bvv.Keyframe

Names of visible actors (e.g.

visibleSize() - Method in class sc.fiji.snt.seed.SeedOverlay

VisitingZoom() - Constructor for class sc.fiji.snt.gui.GuiUtils.JTables.VisitingZoom

VisitingZoom(int) - Constructor for class sc.fiji.snt.gui.GuiUtils.JTables.VisitingZoom

vmAxial() - Method in record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.Report

Returns the value of the vmAxial record component.

vmDirectional() - Method in record class sc.fiji.snt.analysis.sholl.math.PolarProfileStats.Report

Returns the value of the vmDirectional record component.

VOLUME - Static variable in interface sc.fiji.snt.analysis.sholl.math.ShollStats

Flag for volume normalization (Semi-log/Log-log method)

VOLUME - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying Volume statistics.

VonMisesFit(double, double, double, CircularModels.Domain) - Constructor for record class sc.fiji.snt.analysis.CircularModels.VonMisesFit

Creates an instance of a VonMisesFit record class.

voxelSize - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

W

WAITING_FOR_SIGMA_POINT_I - Static variable in class sc.fiji.snt.SNTUI

waitingForRoiDrawing - Variable in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

warn(String) - Static method in class sc.fiji.snt.SNTUtils

warn(String) - Method in class sc.fiji.snt.util.Logger

Logs a warning message.

Warning(String, PlausibilityCheck.Severity, String, PointInImage, List<Path>, double, double) - Constructor for record class sc.fiji.snt.analysis.curation.PlausibilityCheck.Warning

Compact constructor: guarantees affectedPaths is never null.

WARNING - Enum constant in enum class sc.fiji.snt.analysis.curation.PlausibilityCheck.Severity

Warning: the operation is suspect and likely an error.

warningColor() - Static method in class sc.fiji.snt.gui.EnhancedGenericDialog

Deprecated.

warningColor() - Static method in class sc.fiji.snt.gui.GuiUtils

warningsUpdated(List<PlausibilityCheck.Warning>) - Method in interface sc.fiji.snt.analysis.curation.PlausibilityMonitor.WarningListener

Called whenever the monitor's warning list is updated.

warningsUpdated(List<PlausibilityCheck.Warning>) - Method in class sc.fiji.snt.CurationManager

WAYPOINT - Enum constant in enum class sc.fiji.snt.tracing.auto.AutoTracer.SeedRole

Intermediate constraint: path should pass through / near this.

WekaModelLoader - Class in sc.fiji.snt.io

GUI command for Loading pre-trained models from Labkit/TWS as secondary image layer.

WekaModelLoader() - Constructor for class sc.fiji.snt.io.WekaModelLoader

width - Variable in class sc.fiji.snt.SNT

width() - Method in class sc.fiji.snt.util.BoundingBox

WIDTH - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

WIDTH - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Width"

WINDOWS - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

WINDOWS2 - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

windowSize(int) - Method in class sc.fiji.snt.analysis.detection.AlongPathDetector.Config

Sets AlongPathDetector.Config.windowSize.

wipe() - Static method in class sc.fiji.snt.gui.cmds.PrefsCmd

withinBounds(int, int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

withinThreshold(double) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

withinXYbounds(int, int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

withinZbounds(int) - Method in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

WIZARD - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

WORD_BUTTON - Static variable in class sc.fiji.snt.gui.SearchField

wordButton() - Method in class sc.fiji.snt.gui.SearchField

workspaceIsValid() - Method in class sc.fiji.snt.SNTPrefs

wrapWithAxes(RandomAccessibleInterval<T>, ImgPlus<?>, String) - Static method in class sc.fiji.snt.util.ImgUtils

Wrap a RandomAccessibleInterval with axis metadata from a source ImgPlus.

wrapWithSpacing(RandomAccessibleInterval<?>, double[]) - Static method in class sc.fiji.snt.util.ImgUtils

Wraps a RandomAccessibleInterval as an ImgPlus with calibrated axes (no unit).

wrapWithSpacing(RandomAccessibleInterval<?>, double[], String) - Static method in class sc.fiji.snt.util.ImgUtils

Wraps a RandomAccessibleInterval as an ImgPlus with calibrated axes.

writeBdvN5Xml(File, String, long[][], double[], String, int, String) - Static method in class sc.fiji.snt.io.SpimDataUtils

Writes a BDV-compatible XML descriptor for an N5 dataset.

writeBdvN5Xml(File, String, long[][], double[], String, int, String, int) - Static method in class sc.fiji.snt.io.SpimDataUtils

writeNodesXML(PrintWriter) - Method in class sc.fiji.snt.Fill

writeXML(PrintWriter, int) - Method in class sc.fiji.snt.Fill

writeXML(String, boolean) - Method in class sc.fiji.snt.PathAndFillManager

X

x - Variable in class sc.fiji.snt.analysis.detection.Detection

X-coordinate of the detection in real-world units

x - Variable in class sc.fiji.snt.analysis.PCAnalyzer.PrincipalAxis

The X component of the axis direction

x - Variable in class sc.fiji.snt.Fill.Node

x - Variable in class sc.fiji.snt.seed.SeedPoint

Physical X coordinate (calibrated).

x - Variable in class sc.fiji.snt.tracing.DefaultSearchNode

x - Variable in class sc.fiji.snt.util.CircleCursor3D

x - Variable in class sc.fiji.snt.util.CrossoverFinder.CrossoverEvent

X-coordinate of crossover center in real world units

x - Variable in class sc.fiji.snt.util.PointInImage

The cartesian coordinate of this node

X - Enum constant in enum class sc.fiji.snt.viewer.Viewer3D.RotationAxis

Rotation around the X-axis (elevation sweep from front).

X_AXIS - Static variable in class sc.fiji.snt.Tree

X_COORDINATES - Static variable in class sc.fiji.snt.analysis.NodeColorMapper

Flag for "X coordinates" statistics.

X_COORDINATES - Static variable in class sc.fiji.snt.analysis.NodeStatistics

Flag for "X coordinates" statistics.

X_COORDINATES - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: X coordinates

X_COORDINATES - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "X coordinates"

X_RAY - Enum constant in enum class sc.fiji.snt.gui.IconFactory.GLYPH

x_spacing - Variable in class sc.fiji.snt.Fill

x_spacing - Variable in class sc.fiji.snt.Path

x_spacing - Variable in class sc.fiji.snt.SNT

x_spacing - Variable in class sc.fiji.snt.tracing.TubularGeodesicsTracer

X_VALUES - Static variable in class sc.fiji.snt.analysis.PathProfiler

Key for retrieving distances from PathProfiler.getValues(Path)

xBasis - Variable in class sc.fiji.snt.util.CircleCursor3D

xc - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

xMax - Variable in class sc.fiji.snt.tracing.AbstractSearch

xMin - Variable in class sc.fiji.snt.tracing.AbstractSearch

xSep - Variable in class sc.fiji.snt.tracing.AbstractSearch

xSeparationFromPreviousPoint() - Method in class sc.fiji.snt.util.SWCPoint

Returns the X-distance from previous point.

xSpacing - Variable in class sc.fiji.snt.util.BoundingBox

The 'voxel width' of the bounding box

xVec - Variable in class sc.fiji.snt.util.CircleCursor3D

xy - Variable in class sc.fiji.snt.hyperpanes.MultiDThreePanes

XY - Enum constant in enum class sc.fiji.snt.viewer.Viewer3D.ViewMode

Enforce a XY view point of the scene.

xy_canvas - Variable in class sc.fiji.snt.hyperpanes.MultiDThreePanes

XY_PLANE - Static variable in class sc.fiji.snt.analysis.RoiConverter

SNT's XY view (the default export plane)

XY_PLANE - Static variable in class sc.fiji.snt.hyperpanes.MultiDThreePanes

SNT's XY view

xy_window - Variable in class sc.fiji.snt.hyperpanes.MultiDThreePanes

xyzct() - Method in class sc.fiji.snt.analysis.detection.Detection

Returns the XYZCT coordinates for bookmark/ROI integration.

xyzct() - Method in class sc.fiji.snt.util.CrossoverFinder.CrossoverEvent

The XYZCT locations (ImagePlus nomenclature with ZCT 1-based indices) of the event center.

xz - Variable in class sc.fiji.snt.hyperpanes.MultiDThreePanes

XZ - Enum constant in enum class sc.fiji.snt.viewer.Viewer3D.ViewMode

Enforce a XZ view point of the scene.

xz_canvas - Variable in class sc.fiji.snt.hyperpanes.MultiDThreePanes

XZ_PLANE - Static variable in class sc.fiji.snt.analysis.RoiConverter

SNT's XZ view

XZ_PLANE - Static variable in class sc.fiji.snt.hyperpanes.MultiDThreePanes

SNT's XZ view

xz_window - Variable in class sc.fiji.snt.hyperpanes.MultiDThreePanes

Y

y - Variable in class sc.fiji.snt.analysis.detection.Detection

Y-coordinate of the detection in real-world units

y - Variable in class sc.fiji.snt.analysis.PCAnalyzer.PrincipalAxis

The Y component of the axis direction

y - Variable in class sc.fiji.snt.Fill.Node

y - Variable in class sc.fiji.snt.seed.SeedPoint

Physical Y coordinate (calibrated).

y - Variable in class sc.fiji.snt.tracing.DefaultSearchNode

y - Variable in class sc.fiji.snt.util.CircleCursor3D

y - Variable in class sc.fiji.snt.util.CrossoverFinder.CrossoverEvent

Y-coordinate of crossover center in real world units

y - Variable in class sc.fiji.snt.util.PointInImage

The cartesian coordinate of this node

Y - Enum constant in enum class sc.fiji.snt.viewer.Viewer3D.RotationAxis

Rotation around the Y-axis (elevation sweep from side).

Y_AXIS - Static variable in class sc.fiji.snt.Tree

Y_COORDINATES - Static variable in class sc.fiji.snt.analysis.NodeColorMapper

Flag for "Y coordinates" statistics.

Y_COORDINATES - Static variable in class sc.fiji.snt.analysis.NodeStatistics

Flag for "Y coordinates" statistics.

Y_COORDINATES - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Y coordinates

Y_COORDINATES - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Y coordinates"

y_spacing - Variable in class sc.fiji.snt.Fill

y_spacing - Variable in class sc.fiji.snt.Path

y_spacing - Variable in class sc.fiji.snt.SNT

y_spacing - Variable in class sc.fiji.snt.tracing.TubularGeodesicsTracer

Y_VALUES - Static variable in class sc.fiji.snt.analysis.PathProfiler

Key for retrieving intensities from PathProfiler.getValues(Path)

yBasis - Variable in class sc.fiji.snt.util.CircleCursor3D

yc - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

yesNoDialog(String, String) - Method in class sc.fiji.snt.gui.GuiUtils

yesNoDialog(String, String, String, String) - Method in class sc.fiji.snt.gui.GuiUtils

yesNoHTMLDialog(String, String, String, String) - Method in class sc.fiji.snt.gui.GuiUtils

yesNoPrompt(String, String) - Method in class sc.fiji.snt.gui.GuiUtils

yMax - Variable in class sc.fiji.snt.tracing.AbstractSearch

yMin - Variable in class sc.fiji.snt.tracing.AbstractSearch

ySep - Variable in class sc.fiji.snt.tracing.AbstractSearch

ySeparationFromPreviousPoint() - Method in class sc.fiji.snt.util.SWCPoint

Returns the Y-distance from previous point.

ySpacing - Variable in class sc.fiji.snt.util.BoundingBox

The 'voxel height' of the bounding box

yVec - Variable in class sc.fiji.snt.util.CircleCursor3D

YZ - Enum constant in enum class sc.fiji.snt.viewer.Viewer3D.ViewMode

Enforce a YZ view point of the scene.

Z

z - Variable in class sc.fiji.snt.analysis.detection.Detection

Z-coordinate of the detection in real-world units

z - Variable in class sc.fiji.snt.analysis.PCAnalyzer.PrincipalAxis

The Z component of the axis direction

z - Variable in class sc.fiji.snt.Fill.Node

z - Variable in class sc.fiji.snt.seed.SeedPoint

Physical Z coordinate (calibrated). 0 for 2D images.

z - Variable in class sc.fiji.snt.tracing.DefaultSearchNode

z - Variable in class sc.fiji.snt.util.CrossoverFinder.CrossoverEvent

Z-coordinate of crossover center in real world units

z - Variable in class sc.fiji.snt.util.PointInImage

The cartesian coordinate of this node

Z - Enum constant in enum class sc.fiji.snt.viewer.Viewer3D.RotationAxis

Rotation around the Z-axis (azimuth sweep).

Z_AXIS - Static variable in class sc.fiji.snt.Tree

Z_COORDINATES - Static variable in class sc.fiji.snt.analysis.NodeColorMapper

Flag for "Z coordinates" statistics.

Z_COORDINATES - Static variable in class sc.fiji.snt.analysis.NodeStatistics

Flag for "Z coordinates" statistics.

Z_COORDINATES - Static variable in class sc.fiji.snt.analysis.TreeColorMapper

Mapping property: Z coordinates

Z_COORDINATES - Static variable in class sc.fiji.snt.analysis.TreeStatistics

Flag specifying "Z coordinates"

z_spacing - Variable in class sc.fiji.snt.Fill

z_spacing - Variable in class sc.fiji.snt.Path

z_spacing - Variable in class sc.fiji.snt.SNT

z_spacing - Variable in class sc.fiji.snt.tracing.TubularGeodesicsTracer

ZBAtlasUtils - Class in sc.fiji.snt.annotation

Utility methods for accessing the Max Plank Zebrafish Brain Atlas (ZBA) at fishatlas.neuro.mpg.de.

zc - Variable in class sc.fiji.snt.analysis.sholl.parsers.ImageParser

zeroCounts() - Method in class sc.fiji.snt.analysis.sholl.Profile

zigzagRemovalEnabled - Variable in class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

zMax - Variable in class sc.fiji.snt.tracing.AbstractSearch

zMin - Variable in class sc.fiji.snt.tracing.AbstractSearch

zoom100PercentAllPanes() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

zoomAllPanes(double) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

zoomEventOccurred(boolean, int, int, int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes

zoomEventOccurred(boolean, int, int, int) - Method in interface sc.fiji.snt.hyperpanes.PaneOwner

Called when a zoom event occurs.

zoomIn(int, int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

zoomOut(int, int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas

zoomTo(ImagePlus, double, int, int) - Static method in class sc.fiji.snt.util.ImpUtils

zoomTo(ImagePlus, double, Collection<Path>, int) - Static method in class sc.fiji.snt.util.ImpUtils

Zooms the image canvas to the specified magnification level, centered on the bounding box of the given paths.

zoomTo(ImagePlus, double, PointInImage, Path) - Static method in class sc.fiji.snt.util.ImpUtils

Zooms the image canvas to a specific location on a path, correctly accounting for the path's canvas offset.

zoomTo(ImagePlus, Collection<Path>) - Static method in class sc.fiji.snt.util.ImpUtils

Zooms the image canvas to optimally display the specified paths in the XY plane.

zoomTo(ImagePlus, Collection<Path>, int) - Static method in class sc.fiji.snt.util.ImpUtils

Zooms the image canvas to optimally display the specified paths in the given plane.

zoomTo(Object...) - Method in class sc.fiji.snt.viewer.Viewer3D

Zooms the scene into the bounding box enclosing the specified objects.

zScore(double) - Method in class sc.fiji.snt.tracing.cost.OneMinusErf

zSep - Variable in class sc.fiji.snt.tracing.AbstractSearch

zSeparationFromPreviousPoint() - Method in class sc.fiji.snt.util.SWCPoint

Returns the Z-distance from previous point.

zSlice() - Method in record class sc.fiji.snt.tracing.auto.SomaUtils.SomaResult

Returns the value of the zSlice record component.

zSpacing - Variable in class sc.fiji.snt.util.BoundingBox

The 'voxel depth' of the bounding box

zy - Variable in class sc.fiji.snt.hyperpanes.MultiDThreePanes

zy_canvas - Variable in class sc.fiji.snt.hyperpanes.MultiDThreePanes

ZY_PLANE - Static variable in class sc.fiji.snt.analysis.RoiConverter

SNT's ZY view

ZY_PLANE - Static variable in class sc.fiji.snt.hyperpanes.MultiDThreePanes

SNT's ZY view

zy_window - Variable in class sc.fiji.snt.hyperpanes.MultiDThreePanes

_

_extraButtons - Variable in class sc.fiji.snt.gui.SNTSearchableBar

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