Package sc.fiji.snt.plugin

package sc.fiji.snt.plugin

SNT add-ons as IJ2 commands

Author:

Tiago Ferreira

Related Packages

Package	Description
sc.fiji.snt	SNT core classes
sc.fiji.snt.plugin.ij1	SNT add-ons as legacy ("IJ1") plugins.

Classes

Class	Description
AnalyzerCmd	Deprecated. replaced by MeasureUI
AnnotationDensityCmd	Command for obtaining spine/varicosity/synapse/etc. counts from multipoint ROIs or bookmarked locations
AutotraceFromBinarySeedsCmd	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.
AutotraceFromBinaryTipsCmd	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.
AutotraceFromSeedsCmd	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).
AutotraceFromTipsCmd	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.
AutotraceFromWaypointsCmd	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.
BinaryTracerCmd	Interactive command providing a GUI for BinaryTracer-based autotracing when an image is already loaded in SNT.
BinaryTracerCommonCmd	Abstract base command providing shared parameters and logic for BinaryTracer-based autotracing.
BinaryTracerFileCmd	Non-interactive command for batch BinaryTracer autotracing of all images in a directory.
BrainAnnotationCmd	Command to perform distribution analysis of BrainAnnotations on an annotated Tree.
ChooseDataset	Implements "Choose New Dataset" command for SNTUI.
ConvexHullCmd	Implements the "Convex Hull Analysis..." command.
GraphAdapterMapperCmd	Command for mapping colors to graph nodes and edges based on specified properties and visualization parameters.
GroupAnalyzerCmd	Command for Comparing Groups of Tree(s).
GrowthAnalyzerCmd	GUI command to the GrowthAnalyzer class.
GWDTMultiSomaCmd	Interactive command for multi-soma GWDT autotracing.
GWDTMultiSomaCommonCmd	Abstract base for multi-soma GWDT autotracing commands.
GWDTMultiSomaFileCmd	Non-interactive command for file-based multi-soma GWDT autotracing with support for single images or batch processing of a directory.
GWDTTracerCmd	Interactive command providing a GUI for GWDT autotracing when an image is already loaded in SNT.
GWDTTracerCommonCmd	Base command providing shared parameters and logic for GWDT autotracing.
GWDTTracerFileCmd	Non-interactive command for file-based GWDT autotracing with support for single images or batch processing of an entire directory.
InterpolateRadiiCmd	Command for finding all the nodes in a collection of paths with invalid radius, and assign them interpolated values from their neighbors and Viewer3D
LabkitLoaderCmd	Command for sending Path-converted ROIs to a new Labkit instance.
LocalThicknessCmd	Convenience command for running Fiji's "Local Thickness" plugin from SNT, enabling estimation of radii from binary skeleton images.
PathAnalyzerCmd	Command for measuring Paths in isolation.
PathMatcherCmd	Command for matching Paths across time-points (time-lapse analysis).
PathOrderAnalysisCmd	Command to perform Path Ordering analysis on a Tree.
PathSpineAnalysisCmd	Command for obtaining plots pertaining to spine/varicosity counts
PathTimeAnalysisCmd	Command for obtaining 'time-profiles' of Paths (time-lapse analysis).
PlotterCmd	Implements Reconstruction Plotter, a command wrapper for interactively plotting trees using Viewer2D
ROIExporterCmd	Command providing a GUI for RoiConverter and allowing export of Paths to the IJ1 ROI Manager.
RootAngleAnalyzerCmd	Command to perform Root angle analysis on a collection of Trees
ShollAnalysisBulkTreeCmd	A modified version of ShollAnalysisTreeCmd for Bulk Sholl Analysis.
ShollAnalysisImgCmd	Command for performing Sholl analysis on binary 2D/3D images of neuronal structures.
ShollAnalysisImgCommonCmd	Implements the backbone for Analyze:Sholl:Sholl Analysis (From Image) commands...
ShollAnalysisImgInteractiveCmd	Interactive command for performing Sholl analysis on binary 2D/3D images, with real-time parameter adjustment and visualization updates.
ShollAnalysisPrefsCmd	Implements the "Sholl Options" command
ShollAnalysisTreeCmd	Implements SNT's commands for Sholl Analysis of Trees.
ShollAnalysisTreeInteractiveCmd	Interactive command for performing Sholl analysis on reconstructed neuronal tracings, with real-time parameter adjustment and interactive visualization.
SkeletonizerCmd	Convenience command for converting Paths into skeleton images
SomaDetectorCmd	Command to automatically detect the soma (cell body) in neuronal images.
StrahlerCmd	Command to perform Horton-Strahler analysis on a collection of Trees
TreeMapperCmd	Command for color coding trees according to their properties and statistics, using MultiTreeColorMapper and TreeColorMapper.
TWSLoaderCmd	Command for sending Path-converted ROIs to a new TWS instance.