All Classes and Interfaces
Class
Description
Abstract base class for grayscale-based automatic neuron tracers.
Parent class for convex hull analysis
Abstract base class for GWDT-based tracers: APP2-style neuron tracer using Gray-Weighted
Distance Transform and Fast Marching.
Represents a hierarchical segment as defined by APP2.
How the per-waypoint bias amount is derived.
Abstract class for path-finding over
RandomAccessibleIntervalsImplements Reconstruction Viewer's 'Add Annotation Label...' commands.
Defines an Allen Reference Atlas (ARA) [Allen Mouse Common Coordinate
Framework] annotation.
Utility methods for accessing/handling
AllenCompartmentsDetects features (boutons, varicosities) along traced paths by
analyzing longitudinal radius and intensity profiles.
Configuration for along-path detection with builder-like setters.
SciJava command for detecting boutons/varicosities along traced paths using
longitudinal radius and intensity profiles.
Static utilities for sc.fiji.analysis.
Deprecated.
Command for obtaining spine/varicosity/synapse/etc. counts from multipoint ROIs or
bookmarked locations
A specialized graph implementation for brain annotations that extends
SNTGraph.JGraphX adapter for visualizing annotation graphs with brain structures as vertices.
JGraphX visualization component for annotation graphs.
SciJava Command for assembling brain annotation connectivity diagrams from
tagged neurons, depicting semi-quantitative summaries of targeted brain areas.
SciJava Command for displaying annotation graph data in the Reconstruction Viewer
with customizable color metrics and mesh opacity.
Utilities for AnnotationGraph handling and manipulation.
A specialized
ColorMapper for applying color-coded mappings to 3D annotations.Represents a weighted edge between two
BrainAnnotation vertices in an annotation graph.In-memory array storage backend using ImgLib2 ArrayImgs.
Derives
AbstractGWDTTracer configuration parameters from one or more
example paths.Non-modal dialog displaying
AutoTraceConfig results in a JTable with
checkboxes, allowing the user to cherry-pick which derived parameters to apply.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.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.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).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.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.Interface for automatic neuron tracers that reconstruct complete neuronal
morphologies from images.
Role a
SeedPoint plays in a tracing run.Manages Tracing Backup files in the workspace.
Class for generation of
Trees from a skeletonized image.Interactive command providing a GUI for
BinaryTracer-based
autotracing when an image is already loaded in SNT.Abstract base command providing shared parameters and logic for
BinaryTracer-based autotracing.Non-interactive command for batch
BinaryTracer
autotracing of all images in a directory.A flexible implementation of the bidirectional heuristic search algorithm described in
Pijls, W.H.L.M., Post, H., 2009.
An artist implementation that visualizes bidirectional search operations.
A
SearchNode which can maintain both a from-start and from-goal search state.Implements the Bookmark Manager pane.
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.Classes extending this interface implement a neuropil label/annotation aka
"compartment".
Command to perform distribution analysis of
BrainAnnotations on an
annotated Tree.Support for Big Volume Viewer.
Renders spherical annotations at
SNTPoint world coordinates.A snapshot of the BVV viewer state at a particular moment, used as a
keyframe for movie recording.
Configuration options for path rendering.
Convenience command for starting a standalone Bvv instance.
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.Command providing a GUI for configuring
Bvv.PathRenderingOptions.A custom GUI component combining a checkbox and spinner control in a single panel.
Implements "Choose New Dataset" command for SNTUI.
Implements the 'Choose Tracing Image (From Open Image)...' command.
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.
Shared utilities for circular modeling, including von Mises fits.
Domain of the angle data.
Immutable summary of a von Mises fit on circular (directional) or axial (orientation) data.
A user-triggered collapsible panel.
Interface for monitoring changes in
ColorChooserButton.Creates a JButton holding a color chooser.
Parent class for ColorMappers.
Implements Reconstruction Viewer's 'Color coding' commands.
Utilities for colormaps and IJ lookup tables
Generates a simplified color widget holding both predetermined colors and
user-defined ones.
Command class for GUI commands extending DynamicCommand
Compares two profiles statistically.
Command for opening two SWC/traces files in a dedicated Reconstruction
Viewer.
This class allows you to move a Component by using a mouse.
Bridges gaps between disconnected components of an auto-traced neuron tree.
Implements the "Generate Secondary Layer" command.
Computes the convex hull of a set of 2D points.
Convex hull analysis in 3D.
Class for Convex Hull measurements of a
Tree.Implements the "Convex Hull Analysis..." command.
Interface for cost function implementations used by
SearchInterfaceEntry-point command for the cost-function wizard.
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.Listener notified when the user picks (or cancels).
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.
Immutable configuration with builder-like setters.
One detected crossover event.
Static utilities for computing cross-sectional planes perpendicular to a path
tangent.
Implements the Curation Assistant pane in SNT's UI.
Reserved
cur:* path tags used to record a path's review status
after it has been examined in the Curation Assistant.Four-bucket breakdown returned by
CurationTags.partitionByReviewStatus(Tree).Command for customizing axis-to-anatomy mappings in Reconstruction Viewer.
Command for customizing a LUT legend in Reconstruction Viewer
Command for customizing an OBJ mesh in Reconstruction Viewer
Command for customizing selected Trees in Reconstruction Viewer.
A
SearchNode which can maintain both a from-start and from-goal search state.Implements the Delineation Analysis pane.
Manages loading and running of demonstration datasets and reconstructions in SNT.
One detected feature along or around a traced path (varicosity, spine,
bouton, punctum, etc.).
Shared utilities for path-based detectors (
PeripathDetector,
AlongPathDetector).Cost function that computes path cost based on the difference between voxel values
and a specified range, useful for tracing along intensity gradients.
A
Heuristic that always returns zero, reducing A* search to Dijkstra's algorithm.Class for accessing a reconstruction as a graph structure.
Class for accessing the sub-graph that has a subset of vertices and a subset
of edges of a
DirectedWeightedGraph.Disk-backed GWDT tracer for very large images.
Disk-backed storage backend for very large images.
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.
Command for plotting distributions of morphometric properties
(branch-related) of
TreesCommand for plotting distributions of whole-cell morphometric properties of
TreesRepresents a brain region from the Drosophila Anatomy Ontology (FBbt).
Utility methods for accessing the Drosophila adult brain ontology
derived from FBbt (Drosophila Anatomy Ontology).
GUI command for duplicating a Path.
Implements the 'EnableSciViewUpdateSite' command.
Deprecated.
A* search heuristic using euclidean distance from current node to goal node
SciJava Command for creating publication-ready figures of neuronal
reconstructions in 2D and 3D formats with customizable styles and layouts.
Improvements to JFileChooser, namely:
This class makes it easy to drag and drop files from the operating system to
a Java program.
Implement this inner interface to listen for when files are dropped.
A FilePicker panel similar to Scijava's File widget but adopting SNT's FileChooser.
Defines a filled structure.
Defines a node in a filled structure.
The
FillerProgressCallback interface extends SearchProgressCallback
and provides additional methods specific to monitoring the progress of filler algorithms.Seeded-volume segmentation via single-source shortest paths.
An artist class that visualizes the progress and behavior of fill operations
performed by filler threads.
Implements the Fill Manager dialog.
Implements
PathManagerUI's "Extension Angle(s)" prompt.Absurdly simple importer for retrieving SWC data from
FlyCircuit.
A.F.
Command for mapping colors to graph nodes and edges based on specified properties
and visualization parameters.
A color mapping utility for graph visualization that assigns colors to vertices and edges
based on various graph metrics.
Main editor panel for interactive visualization and manipulation of SNT graphs.
Command for displaying the contents of Path Manager in the "SNT Graph Viewer"
Utilities for Graph handling.
Provides a graphical user interface for visualizing
and interacting with graphs using SNT's "Graph Viewer".
Command for Comparing Groups of Tree(s).
Computes statistics from
Tree groups.Container class for growth analysis results from
GrowthAnalyzer, serving as the
primary interface for accessing growth analysis results.Container for summary statistics across all analyzed neurites.
Interface for defining neurite selection criteria.
Core analyzer for time-lapse growth analysis of neuronal paths.
Represents an elongation event
Represents a growth phase with specific characteristics
Types of growth phases
Represents a retraction event
Represents a single time point measurement
GUI command to the
GrowthAnalyzer class.Misc. utilities for SNT's GUI.
Utility methods for
JTable configuration and creation.Stateful helper that extracts a
JScrollPane from its current
parent into a free-floating, modeless JDialog, and re-attaches
it on demand.Stateful "visiting zoom" helper used by table panels that navigate
the canvas on double-click (BookmarkManager, CurationManager,
SeedOverlayPanel).
Interactive command for multi-soma GWDT autotracing.
Abstract base for multi-soma GWDT autotracing commands.
Non-interactive command for file-based multi-soma GWDT autotracing with
support for single images or batch processing of a directory.
In-memory GWDT tracer using array storage.
Interactive command providing a GUI for GWDT autotracing when an image is
already loaded in SNT.
Base command providing shared parameters and logic for GWDT autotracing.
Factory for creating optimal GWDT tracer implementations based on image size.
Non-interactive command for file-based GWDT autotracing with support for
single images or batch processing of an entire directory.
Represents a callback interface for monitoring the progress of Hessian filtering.
Interface for heuristic estimates to the goal used by classes implementing
SearchInterface.A factory for
FADerivedIcons presets.A
Parser for extracting Sholl profiles from image data.Sholl Parser for 2D images
Parser for 3D images
Static utilities for handling and manipulation of
RandomAccessibleIntervalsResult of a channel/time slice extraction from an
ImgPlus.Imports candidate seed points from a CSV file into SNT's
SeedOverlay.Static utilities for handling and manipulation of
ImagePlussCommand for importing InsectBrain reconstructions
Methods for retrieving reconstructions and annotations from the Insect Brain Database at
insectbraindb.org *
Utility methods for retrieving species, brain, and neuron data from
the Insect Brain Database
Command for finding all the nodes in a collection of paths with invalid
radius, and assign them interpolated values from their neighbors and
Viewer3DCommand for importing a (MouseLight) JSON file
Detects contact points between traced paths and labeled surfaces (from a
segmentation/label image).
Configuration for
LabelProximityDetector.SciJava command for detecting proximity contacts between traced paths and labeled surfaces (segmentation images).
Helper that turns a labels image (e.g. cellpose, Labkit, StarDist
segmentation output) into a list of
SeedPoints, one per non-zero
label.Command for sending Path-converted ROIs to a new Labkit instance.
Static helpers for creating lazy filtered images
Static methods for linear algebra
Retrieves descriptive statistics and calculates Sholl Metrics from sampled
Sholl profiles, including those relying on polynomial fitting.
A
SearchImage backed by an ImgLib2 ListImg, providing
list-based storage for path-search data structures.Command for loading an OBJ file in Reconstruction Viewer
Command for loading Reconstruction files in Reconstruction Viewer.
Generates
SeedPoints from an open labels image (e.g. cellpose,
Labkit, StarDist masks).Generates
SeedPoints from the contents of the RoiManager.Convenience command for running Fiji's "Local Thickness" plugin from SNT, enabling
estimation of radii from binary skeleton images.
The Logger class provides functionality for logging messages with different levels such as
info, debug, and warn.
Lindenmayer systems utilities for rendering fractal trees using L-system rules
for generating and visualizing self-similar branching structures.
A tracer thread for manual tracing.
A sparse matrix implementation backed by a
Long2ObjectOpenHashMapThe MeasureUI class is a graphical user interface for measuring and analyzing
Trees.Command for importing MouseLight reconstructions
Methods for retrieving reconstructions from MouseLight's online database at
ml-neuronbrowser.janelia.org *
Importer for retrieving reconstructions from MouseLight's online database at
ml-neuronbrowser.janelia.org
Convenience class defining methods common to SNT's XY, XZ, and ZY panes
Canvas for displaying and interacting with multiple planes in 3D space,
providing synchronized visualization and navigation across orthogonal projections.
TracerCanvas variant that renders a caller-supplied collection of Paths: each in its own color,
with one entry optionally "highlighted".One painted path: the path itself, its base color, and whether to highlight it
Post-hoc refinement of traced paths in multispectral (e.g., Brainbow) images.
Immutable parameter set for multispectral refinement.
GUI command for
MultiSpectralRefiner.Command for importing a folder of SWC files.
Class for color coding groups of
Trees.Computes summary and descriptive statistics from univariate properties of
Tree groups.Class for rendering montages of
Trees as 2D plots that can be exported as SVG, PNG or PDF.Class for rendering individual
Viewer3Ds as a multi-panel montage.Circle layout algorithm for grouped annotation graph visualization.
SciJava Command implementing grouped circular layout algorithm for graph
visualization with multi-level organizational hierarchy support.
A circle layout that is more compact than the default
mxCircleLayout by applying a 'reduction factor' to the layout radius.Sorted circle layout algorithm for SNT graphs.
Command for setting parameters of the mxOrganicLayout Graph layout used in GraphEditor.
Importer for NeuronJ data files.
Command for importing a NeuronJ NDF file.
This class encapsulates the relationship between an arbitrary point
(nearPoint.x,nearPoint.y,nearPoint.z) close to a particular point on a
particular path.
Data container for growth analysis results of a single neurite over time.
Importer for Neurolucida XML files (Neuromorphological File Specification /
NMF format).
Importer for retrieving SWC data from neuromorpho.org.
GUI for "New Graph Options" Command
Class for color coding of
NodeStatistics results.Command to retrieve node profiles (plots of voxel intensities sampled across
Path nodes).
Computes summary and descriptive statistics from a Collection of nodes, including convenience methods to plot
distributions of such data.
Calculates Sholl Metrics from normalized profiles, including Sholl decay and
methods for determination of 'optimal' normalization.
Implements the Notepad pane.
An OBJMesh stores information about a Wavefront .obj mesh loaded
into
Viewer3D, with access points to its OBJFile and
DrawableVBOUtility for setting ImgPlus axes from OME metadata (OME-XML or OME-Zarr).
Parsed OME metadata container.
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
A reusable panel that presents one or more hierarchical ontologies as
searchable checkbox trees.
Default cell renderer for Allen CCF ontology trees.
Implements the 'Choose Tracing Image (From File)...' command.
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).Interface for objects that own and manage multi-pane displays, handling
mouse interactions, zoom events, and pan events across multiple viewing planes.
Interface for parsing data sources to extract Sholl analysis profiles.
This class represents a traced segment (i.e., a Path) in a
reconstruction.
Enhanced PointInImage that stores all node-specific properties.
Command for measuring Paths in isolation.
The PathAndFillManager is responsible for importing, handling and managing of
Paths and Fills.
Iterate over the pixels along the defined nodes of a
PathThis is an implementation of the Ramer-Douglas-Peucker algorithm for
simplifying a curve represented by line-segments, as described here
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.GUI command for
PathFitterImplements the Path Manager Dialog.
Implements the customized SearchableBar used by
PathManagerUI,
including GUI commands for selection and morphological filtering of Paths.Command for matching Paths across time-points (time-lapse analysis).
Convenience class used to render
Path nodes (vertices) in an
TracerCanvas.Command to perform
Path Ordering analysis on a
Tree.Command to retrieve Path profiles (plots of voxel intensities values along a
Path)
Command for obtaining plots pertaining to spine/varicosity counts
A specialized version of
TreeStatistics for analyzing individual paths
without considering their connectivity relationships.Command to "straighten" an image using Path coordinates.
Command for obtaining 'time-profiles' of Paths (time-lapse analysis).
Classes transforming
Paths should implement this interface.Utility class for performing Principal Component Analysis (PCA) on various
SNT data structures including Trees, Paths, and collections of SNTPoints.
Represents a principal axis containing the direction vector and associated
variance (eigenvalue) from Principal Component Analysis.
Detects intensity maxima (varicosities, spines, synaptic puncta) in annular
cross-sections around traced paths.
Deprecated.
Use
PeripathDetector
instead.Immutable configuration with builder-like setters.
Deprecated.
Use
PeripathDetector.Config instead.Deprecated.
Use
Detection instead.SciJava command for detecting varicosities/spines/puncta flanking traced paths.
Performs persistent homology analysis on neuronal
Trees.GUI command persistent homology analyses.
Infers
PlausibilityCheck thresholds from a collection of reference
Trees.Aggregated calibration results from a set of reference trees.
Summary for a single calibrated parameter.
Framework for evaluating the morphological plausibility of path operations
and reconstructions.
Warns when the bifurcation angle at a fork is outside a plausible range.
Warns when a path has radii assigned but they are all identical (likely unfitted defaults).
A heavier check that scans an entire collection of paths for issues.
Warns when the child path's initial direction deviates sharply from
the parent's tangent at the branch point (potential U-turn).
A lightweight check that evaluates the plausibility of a single fork
operation (parent + child + branch index).
Detects paths that run very close to each other without being
topologically connected.
Warns when the child neurite's radius at the fork point exceeds
the parent's radius at the branch point.
Detects abrupt radius jumps between adjacent nodes within a path.
Detects sustained radius increases along a path (neurites should
generally taper distally).
Severity levels for plausibility warnings.
Assesses local image signal quality around traced paths and flags
those in regions with poor contrast.
Warns when a primary path starts far from any soma node.
Warns when a terminal branch is suspiciously short.
Warns when child and parent have very different tortuosity (contraction).
A plausibility warning produced by a check.
Monitors tracing and editing operations for morphological plausibility.
Listener interface for warning list changes.
Implements Reconstruction Plotter, a command wrapper for interactively
plotting trees using
Viewer2DGreedy non-maximum suppression (NMS) for scored 3D points.
Defines a Point in a tracing canvas in pixel coordinates.
Defines a Point in an image, a node of a traced
Path.PolarProfileStats computes angle-resolved (‘Polar Sholl’) metrics from a Sholl Profile,
providing analysis and visualization methods for directional patterns in Sholl profiles.
Simple container for angular peaks.
Immutable summary of the global polar distribution.
Command for (re)setting SNT Preferences.
Defines a Sholl profile
Utility class defining a Sholl profile entry
Profile intensities within local neighborhoods around
Path
PointInImagesAssociates metadata to a Sholl Profile
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.
Command for starting Reconstruction Viewer as a 'stand-alone' program
Command implementing Reconstruction Viewer 'Preferences...' command.
Command for importing SWC reconstructions from remote databases
Importers downloading remote SWC files should extend this interface.
Restores a tracing session including traces, bookmarks, and notes.
Converts SNT
Paths into (IJ1) ROIs.Command providing a GUI for
RoiConverter and allowing export of
Paths to the IJ1 ROI Manager.Class to perform Root angle analysis on a
Tree according to Bird and Cuntz 2019,
PMID 31167149.Command to perform Root angle analysis on a collection of
TreesSaves all open tables, plots, and charts to a specified directory.
Saves a tracing session including traces, bookmarks, notes, tables, charts,
plots, and RM ROIs.
Bridges SNT to
SciView, allowing Trees to be rendered as scenery objectsUtility class for discovery of SNT scripts
A dialog for recording SNT operations as scripts in multiple programming languages
(BeanShell, Groovy, Python).
Interface for classes that draw the progress of a
SearchInterface on a TracerCanvas.Factory for creation of
SearchArtistsAn enhanced text field for search operations with built-in options for case-sensitive,
word-matching, and regex search modes.
General interface for data structures used to keep track
of encountered nodes during image-based searches.
A stack of
SearchImages, backed by a Int2ObjectOpenHashMap.Tracer classes implementing searches between two points should implement this
interface.
Interface representing a node in 3D space that can be used in pathfinding and search algorithms.
Callback interface for monitoring progress of a search operation during path tracing.
Implements a common thread that explores the image using a variety of
strategies, e.g., to trace tubular structures or surfaces.
An artist class responsible for visualizing the progress and state of search threads
during path tracing operations.
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.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).How
SeedOverlayRenderer should pick each seed's LUT slot.Listener fired on any change to the overlay (add/clear/threshold/visibility).
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.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).
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.Bidirectional
SeedPoint-Roi converter.TableModel backed by a SeedOverlay.A modified version of
ShollAnalysisTreeCmd for Bulk Sholl Analysis.Command for performing Sholl analysis on binary 2D/3D images of neuronal structures.
Implements the backbone for Analyze:Sholl:Sholl Analysis (From Image) commands...
Interactive command for performing Sholl analysis on binary 2D/3D images,
with real-time parameter adjustment and visualization updates.
Implements the "Sholl Options" command
Implements SNT's commands for Sholl Analysis of
Trees.Interactive command for performing Sholl analysis on reconstructed neuronal tracings,
with real-time parameter adjustment and interactive visualization.
Class to retrieve Sholl metrics from a
Tree.Renders Sholl analysis results as graphical overlays on an image,
including concentric shells, sampling points, and intersection counts.
An ImageJ
Plot for displaying Sholl analysis profiles, including
sampled data, fitted curves, and descriptive statistics.Convenience flavor of
PointInImage defining 2D/3D points for Sholl Analysis.Methods and constants common to Profile analyzers.
Implementation of
SNTTable for Sholl metrics and Profile lists.Static utilities.
A command that displays a shortcut window of most popular commands, inspired
by the Bio-Formats Plugins Shortcut Window.
Command for highlighting the correspondences between two reconstructions in
the Legacy 3D Viewer
Implements SNT 'Sigma wizard'.
Listener interface for the sigma (gaussian blur standard deviation) palette.
Utility class for computing default Gaussian blur sigma values based on image properties.
Convenience command for converting Paths into skeleton images
Implements the SNT plugin.
Extension of
ChartPanel modified for scientific publications and
convenience methods for plot annotations.A simple class for handling Colors including the ability to map an AWT Color
to a SWC type integer tag.
Implements SNT's Command Palette.
Implements minor customizations to
EditorPane for usage by SNT.Base event class for SNT events.
An abstract weighted graph implementation that extends
AbstractBaseGraph with additional
support for vertex/edge coloring and vertex value mapping.Base adapter that converts SNT graphs to JGraphX graph models for visualization.
Base JGraphX component for SNT graph visualization with interactive controls.
SNT's interpreter UI pane.
SNT's REPL window.
Listener interface for SNT events.
Command for Launching SNT
Classes extend this interface implement a point in a 3D space, always using
real world coordinates.
Class handling SNT preferences.
Syntax-highlighted prompt pane for the SNT scripting REPL.
A specialized implementation of
SNTGraph that represents a directed pseudograph
with weighted edges.JGraphX adapter for visualizing SNT pseudographs (graphs allowing self-loops and multiple edges).
JGraphX visualization component for SNT pseudographs.
SNT's Groovy REPL.
Implements a SearchableBar following SNT's UI.
Service for accessing and scripting the active instance of
SNT.Extension of
DefaultGenericTable with (minor) scripting conveniences.Implements SNT's main dialog.
Static utilities for SNT
Command to automatically detect the soma (cell body) in neuronal images.
Utilities for automatic soma detection and ROI generation.
Container for soma detection results.
Memory-efficient variant of
DirectedWeightedGraph backed by a compressed sparse-row (CSR) adjacency
representation (CsrDirectedSpecifics).Sparse GWDT tracer using hash map storage for memory efficiency.
Sparse storage backend using hash maps for memory-efficient tracing.
Computes a spectral similarity map from a multichannel (e.g., Brainbow) image.
Utilities for working with
AbstractSpimData and BigDataViewer XML
descriptors.Wraps a
RandomAccessibleIntervalSource and overrides
SpimDataUtils.CalibratedSource.getVoxelDimensions() to carry the physical unit (e.g.Implements the 'Open Spot Spine...' command.
Storage backend for GWDT tracing data structures.
This class implements the ImageJ
Strahler Analysis plugin.Class to perform Horton-Strahler analysis on a
Tree.Command to perform Horton-Strahler analysis on a collection of
TreesThis class implements the
Summarize Skeleton command.Static utilities for creation of
Suppliers of SearchImagesImplements a dialog for exporting SWC files.
Exception thrown when an error occurs during SWC file export operations.
Implements a dialog for importing SWC files.
Defines a node in an SWC reconstruction.
Implements
PathManagerUI's SWC-type filtering Command.Implements
PathManagerUI's SWC-SWC-type tagging Options
Command.An extremely simple implementation of a weighted edge for Tree:Directed
Graph conversions.
Utility class that ensures EDT execution.
A
Parser for extracting Sholl profiles from tabular data.Provides rendering capabilities for visualizing paths, overlays, and additional interactive elements
in an ImageJ canvas.
SNT's default tracer thread: explores between two points in an image, doing
an A* search with a choice of distance measures.
Exception thrown when an error occurs while parsing or validating traces file formats.
Implements Reconstruction Viewer's 'Translate...' command.
Utility class to access a Collection of Paths (typically a complete
reconstruction).
Deprecated.
Use
TreeStatistics insteadClass for color coding
Trees.JGraphX adapter for visualizing tree graphs as SWC morphologies.
JGraphX visualization component for tree graphs representing neurite morphologies.
SciJava Command for displaying tree graph structures in the Reconstruction
Viewer as interactive 3D visualizations.
Command for color coding trees according to their properties and statistics,
using
MultiTreeColorMapper and TreeColorMapper.Allows standardized metadata to be associated to a
Tree.Computes summary and descriptive statistics from properties of Paths and Nodes in a
Tree, including
convenience methods to plot distributions of such data.Rasterizes a
Tree into a 3D image using frustum (truncated-cone)
geometry with partial-volume supersampling.Static utilities for Trees.
Result of analyzing which endpoint cluster (starts vs ends) is tighter.
Result of finding the closest endpoints between two paths.
Computes a tubeness (vesselness) filter on a multi-dimensional image using multi-scale
eigenvalue analysis of the Hessian matrix.
A tracer thread for
FijiITKInterface.TubularGeodesics (assumes the
tubularity add-on to be installed)Command for plotting 2D histograms of morphometric distributions
Command for sending Path-converted ROIs to a new TWS instance.
This class is taken directly from
https://github.com/saalfeldlab/hot-knife
Exception thrown when a requested metric is not available or recognized.
Utility methods for accessing/handling Virtual Fly Brain (VFB) annotations
Class for rendering
Trees as 2D plots that can be exported as SVG,
PNG or PDF.Implements SNT's Reconstruction Viewer.
Animation styles for live and recorded rotations.
Axes of rotation for animated sequences and live rotations.
Presets of a scene's view point.
GUI command for Loading pre-trained models from Labkit/TWS as secondary image
layer.
Utility methods for accessing the Max Plank Zebrafish Brain Atlas (ZBA) at
fishatlas.neuro.mpg.de.
MeasureUI