Package sc.fiji.snt

package sc.fiji.snt

SNT core classes

Related Packages

Package	Description
sc.fiji.snt.analysis	Analysis of Trees.
sc.fiji.snt.annotation	Classes handling neuropil annotations and atlases metadata.
sc.fiji.snt.event	Utilities for TrakEM2 interaction
sc.fiji.snt.filter	Filters for detection of tube-like structures
sc.fiji.snt.gui	Customizations and commands for SNT's GUI.
sc.fiji.snt.hyperpanes	Classes implementing SNT's XY, ZY, and XZ canvases.
sc.fiji.snt.io	Classes for importing reconstructions into SNT.
sc.fiji.snt.plugin	SNT add-ons as IJ2 commands
sc.fiji.snt.seed	Classes for Seed Tracing.
sc.fiji.snt.tracing	Path-finding algorithms for interactive neuron tracing.
sc.fiji.snt.util	Miscellaneous SNT utilities, including classes defining reconstruction nodes.
sc.fiji.snt.viewer	Visualization of reconstructions

Class	Description
AStarRefiner	Post-hoc A* re-tracing of a single, already-existing Path: treats the path's current nodes as waypoints and re-derives the geometry between them via SNT.autoTraceSync(List, sc.fiji.snt.util.PointInImage, SNT.SearchSettingsSnapshot), using either the cost function/search parameters currently configured on the active SNT instance, or a frozen SNT.SearchSettingsSnapshot shared across a whole batch (see AStarRefiner(SNT, Path, SNT.SearchSettingsSnapshot)).
BookmarkManager	Implements the Bookmark Manager pane.
CurationManager	Implements the Curation Assistant pane in SNT's UI.
DelineationsManager	Implements the Delineation Analysis pane.
Fill	Defines a filled structure.
Fill.Node	Defines a node in a filled structure.
FillConverter	Map filled nodes from a Collection of FillerThreads to and between RandomAccessibles.
FillConverter.ResultType
FillerProgressCallback	The FillerProgressCallback interface extends SearchProgressCallback and provides additional methods specific to monitoring the progress of filler algorithms.
FillManagerUI	Implements the Fill Manager dialog.
FillManagerUI.State
HessianGenerationCallback	Represents a callback interface for monitoring the progress of Hessian filtering.
MultiPathTracerCanvas	TracerCanvas variant that renders a caller-supplied collection of Paths: each in its own color, with one entry optionally "highlighted".
MultiPathTracerCanvas.Entry	One painted path: the path itself, its base color, and whether to highlight it
NearPoint	This class encapsulates the relationship between an arbitrary point (nearPoint.x,nearPoint.y,nearPoint.z) close to a particular point on a particular path.
NotesUI	Implements the Notepad pane.
Path	This class represents a traced segment (i.e., a Path) in a reconstruction.
Path.PathNode	Enhanced PointInImage that stores all node-specific properties.
PathAndFillManager	The PathAndFillManager is responsible for importing, handling and managing of Paths and Fills.
PathAndFillManager.NodeRef	Immutable reference to a specific node of a specific Path.
PathDownsampler	This is an implementation of the Ramer-Douglas-Peucker algorithm for simplifying a curve represented by line-segments, as described here
PathFitter	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.
PathManagerUI	Implements the Path Manager Dialog.
PathNodeCanvas	Convenience class used to render Path nodes (vertices) in an TracerCanvas.
PathNodeEditor	Viewer-agnostic node-editing operations on a single Path: the logic behind the 'Edit Mode' commands of InteractiveTracerCanvas (delete, insert, move, lock, radius, tag, re-root, split, undo), but free of any canvas/ImagePlus dependency so that it can be driven by other front-ends (e.g., Bdv/Bvv).
PathNodeEditor.Result	Outcome of an edit operation
PathTransformer	Classes transforming Paths should implement this interface.
SciViewSNT	Bridges SNT to SciView, allowing Trees to be rendered as scenery objects
SearchProgressCallback	Callback interface for monitoring progress of a search operation during path tracing.
SeedManager	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.
SeedOverlayRenderer	Stateless renderer that draws a SeedOverlay's seeds onto a TracerCanvas's Graphics2D.
SNT	Implements the SNT plugin.
SNT.CostType
SNT.FilterType
SNT.HeuristicType
SNT.MaterializedCrop	The read-only, EDT-independent half of materializing a region, produced by SNT.buildMaterializedCrop(BoundingBox) and consumed by SNT.installMaterializedCrop(MaterializedCrop).
SNT.SearchImageType
SNT.SearchSettingsSnapshot	Immutable snapshot of the search settings that SNT.createSearch(double, double, double, double, double, double) would otherwise read live from the enclosing SNT instance (SNT.SearchSettingsSnapshot.costType, SNT.SearchSettingsSnapshot.searchImageType, whether tracing on the secondary/filtered image is active).
SNT.SearchType
SNT.VoxelBounds	The result of SNT.resolveVoxelBounds(BoundingBox, Calibration): a world-space region resolved and clamped to voxel-index bounds within this session's streamed source.
SNTPrefs	Class handling SNT preferences.
SNTService	Service for accessing and scripting the active instance of SNT.
SNTUI	Implements SNT's main dialog.
SNTUtils	Static utilities for SNT
SNTUtils.BackgroundTask<T>	Handle to a task submitted via SNTUtils.submitBackground(java.util.concurrent.Callable<T>, java.lang.String): the running Future plus the single-thread ExecutorService backing it, so a caller can wait on the same future repeatedly (e.g. across a retry-prompt loop) and cancel/shut it down exactly once when done with it.
SNTUtils.HeapInfo	Snapshot of JVM heap usage in MB, derived from a single Runtime read.
TracerCanvas	Provides rendering capabilities for visualizing paths, overlays, and additional interactive elements in an ImageJ canvas.
Tree	Utility class to access a Collection of Paths (typically a complete reconstruction).
TreeProperties	Allows standardized metadata to be associated to a Tree.