Class Index#

This page provides an index of all classes available in the SNT API.

Total classes: 76

A#

  • AllenCompartment (sc.fiji.snt.annotation) - Defines an Allen Reference Atlas (ARA) [Allen Mouse Common Coordinate Framework] annotation.

  • AllenUtils (sc.fiji.snt.annotation) - Utility methods for accessing/handling AllenCompartments

  • Annotation3D (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.

B#

  • BiSearch (sc.fiji.snt.tracing) - A flexible implementation of the bidirectional heuristic search algorithm described in Pijls, W.

  • BiSearchNode (sc.fiji.snt.tracing) - A SearchNode which can maintain both a from-start and from-goal search state.

  • BoundingBox (sc.fiji.snt.util) - A BoundingBox contains information (including spatial calibration) of a tracing canvas bounding box, i.

C#

  • ColorMaps (sc.fiji.snt.util) - Utilities for colormaps and IJ lookup tables

  • ConvexHull2D (sc.fiji.snt.analysis) - Computes the convex hull of a set of 2D points.

  • ConvexHull3D (sc.fiji.snt.analysis) - Convex hull analysis in 3D.

  • ConvexHullAnalyzer (sc.fiji.snt.analysis) - Class for Convex Hull measurements of a Tree.

  • CrossoverFinder (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.

D#

  • DefaultSearchNode (sc.fiji.snt.tracing) - A SearchNode which can maintain both a from-start and from-goal search state.

F#

  • Fill (sc.fiji.snt) - Defines a filled structure.

  • FillConverter (sc.fiji.snt) - Map filled nodes from a Collection of FillerThreads to and between RandomAccessibles.

  • FillerThread (sc.fiji.snt.tracing) - Seeded-volume segmentation via single-source shortest paths.

  • FlyCircuitLoader (sc.fiji.snt.io) - Absurdly simple importer for retrieving SWC data from FlyCircuit.

  • Frangi (sc.fiji.snt.filter) - A.

G#

I#

  • ImgUtils (sc.fiji.snt.util) - Static utilities for handling and manipulation of `RandomAccessibleInterval`s

  • ImpUtils (sc.fiji.snt.util) - Static utilities for handling and manipulation of ImagePluss

  • InsectBrainCompartment (sc.fiji.snt.annotation) - Enhanced documentation for InsectBrainCompartment class.

  • InsectBrainLoader (sc.fiji.snt.io) - Methods for retrieving reconstructions and annotations from the Insect Brain Database at insectbraindb.

  • InsectBrainUtils (sc.fiji.snt.annotation) - Utility methods for retrieving species, brain, and neuron data from the Insect Brain Database

  • InteractiveTracerCanvas (sc.fiji.snt) - Enhanced documentation for InteractiveTracerCanvas class.

M#

  • MouseLightLoader (sc.fiji.snt.io) - Methods for retrieving reconstructions from MouseLight’s online database at ml-neuronbrowser.

  • MouseLightQuerier (sc.fiji.snt.io) - Importer for retrieving reconstructions from MouseLight’s online database at ml-neuronbrowser.

  • MultiTreeColorMapper (sc.fiji.snt.analysis) - Class for color coding groups of Trees.

  • MultiTreeStatistics (sc.fiji.snt.analysis) - Computes summary and descriptive statistics from univariate properties of Tree groups.

  • MultiViewer2D (sc.fiji.snt.viewer) - Class for rendering montages of Trees as 2D plots that can be exported as SVG, PNG or PDF.

  • MultiViewer3D (sc.fiji.snt.viewer) - Class for rendering individual Viewer3Ds as a multi-panel montage.

N#

  • NeuroMorphoLoader (sc.fiji.snt.io) - Importer for retrieving SWC data from neuromorpho.

  • NodeColorMapper (sc.fiji.snt.analysis) - Class for color coding of NodeStatistics results.

  • NodeProfiler (sc.fiji.snt.analysis) - Command to retrieve node profiles (plots of voxel intensities sampled across Path nodes).

  • NodeStatistics (sc.fiji.snt.analysis) - Computes summary and descriptive statistics from a Collection of nodes, including convenience methods to plot distributions of such data.

P#

  • Path (sc.fiji.snt) - This class represents a traced segment (i.

  • PathAndFillManager (sc.fiji.snt) - The PathAndFillManager is responsible for importing, handling and managing of Paths and Fills.

  • PathChangeListener (sc.fiji.snt) - Enhanced documentation for PathChangeListener class.

  • PathDownsampler (sc.fiji.snt) - This is an implementation of the Ramer-Douglas-Peucker algorithm for simplifying a curve represented by line-segments, as described here

  • PathFitter (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.

  • PathManagerUI (sc.fiji.snt) - Implements the Path Manager Dialog.

  • PathProfiler (sc.fiji.snt.analysis) - Command to retrieve Path profiles (plots of voxel intensities values along a Path)

  • PathResult (sc.fiji.snt.tracing) - Enhanced documentation for PathResult class.

  • PathStatistics (sc.fiji.snt.analysis) - A specialized version of TreeStatistics for analyzing individual paths without considering their connectivity relationships.

  • PathStraightener (sc.fiji.snt.analysis) - Command to “straighten” an image using Path coordinates.

  • PCAnalyzer (sc.fiji.snt.analysis) - Utility class for performing Principal Component Analysis (PCA) on various SNT data structures including Trees, Paths, and collections of SNTPoints.

  • PersistenceAnalyzer (sc.fiji.snt.analysis) - Performs persistent homology analysis on neuronal Trees.

  • PointInImage (sc.fiji.snt.util) - Defines a Point in an image, a node of a traced Path.

R#

  • RemoteSWCLoader (sc.fiji.snt.io) - Importers downloading remote SWC files should extend this interface.

  • RootAngleAnalyzer (sc.fiji.snt.analysis) - Class to perform Root angle analysis on a Tree according to Bird and Cuntz 2019, PMID 31167149.

S#

  • SciViewSNT (sc.fiji.snt) - Bridges SNT to SciView, allowing Trees to be rendered as scenery objects

  • SearchNode (sc.fiji.snt.tracing) - Enhanced documentation for SearchNode class.

  • SearchThread (sc.fiji.snt.tracing) - Implements a common thread that explores the image using a variety of strategies, e.

  • ShollAnalyzer (sc.fiji.snt.analysis) - Class to retrieve Sholl metrics from a Tree.

  • SkeletonConverter (sc.fiji.snt.analysis) - Class for generation of Trees from a skeletonized ImagePlus.

  • SNT (sc.fiji.snt) - Implements the SNT plugin.

  • SNTChart (sc.fiji.snt.analysis) - Extension of ChartPanel modified for scientific publications and convenience methods for plot annotations.

  • SNTColor (sc.fiji.snt.util) - A simple class for handling Colors including the ability to map an AWT Color to a SWC type integer tag.

  • SNTPoint (sc.fiji.snt.util) - Classes extend this interface implement a point in a 3D space, always using real world coordinates.

  • SNTService (sc.fiji.snt) - Service for accessing and scripting the active instance of SNT.

  • SNTTable (sc.fiji.snt.analysis) - Extension of DefaultGenericTable with (minor) scripting conveniences.

  • SNTUI (sc.fiji.snt) - Implements SNT’s main dialog.

  • SNTUtils (sc.fiji.snt) - Static utilities for SNT

  • StrahlerAnalyzer (sc.fiji.snt.analysis) - Class to perform Horton-Strahler analysis on a Tree.

  • SWCPoint (sc.fiji.snt.util) - Defines a node in an SWC reconstruction.

T#

  • TracerCanvas (sc.fiji.snt) - Provides rendering capabilities for visualizing paths, overlays, and additional interactive elements in an ImageJ canvas.

  • TracerThread (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.

  • Tree (sc.fiji.snt) - Utility class to access a Collection of Paths (typically a complete reconstruction).

  • TreeColorMapper (sc.fiji.snt.analysis) - Class for color coding Trees.

  • TreeProperties (sc.fiji.snt) - Allows standardized metadata to be associated to a Tree.

  • TreeStatistics (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.

  • Tubeness (sc.fiji.snt.filter) - Y.

V#

  • VFBUtils (sc.fiji.snt.annotation) - Utility methods for accessing/handling Virtual Fly Brain (VFB) annotations

  • Viewer2D (sc.fiji.snt.viewer) - Class for rendering Trees as 2D plots that can be exported as SVG, PNG or PDF.

  • Viewer3D (sc.fiji.snt.viewer) - Implements SNT’s Reconstruction Viewer.

W#

  • WekaModelLoader (sc.fiji.snt.io) - GUI command for Loading pre-trained models from Labkit/TWS as secondary image layer.

Z#

  • ZBAtlasUtils (sc.fiji.snt.annotation) - Utility methods for accessing the Max Plank Zebrafish Brain Atlas (ZBA) at fishatlas.

See Also#

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