Uses of Class
sc.fiji.snt.gui.cmds.CommonDynamicCmd

Packages that use CommonDynamicCmd

Package	Description
sc.fiji.snt.analysis	Analysis of Trees.
sc.fiji.snt.gui.cmds	Scijava-based GUIs for SNT built-in commands.
sc.fiji.snt.io	Classes for importing reconstructions into SNT.
sc.fiji.snt.plugin	SNT add-ons as IJ2 commands

Uses of CommonDynamicCmd in sc.fiji.snt.analysis

Subclasses of CommonDynamicCmd in sc.fiji.snt.analysis

Modifier and Type	Class	Description
class	NodeProfiler	Command to retrieve node profiles (plots of voxel intensities sampled across Path nodes).
class	PathProfiler	Command to retrieve Path profiles (plots of voxel intensities values along a Path)

Uses of CommonDynamicCmd in sc.fiji.snt.gui.cmds

Subclasses of CommonDynamicCmd in sc.fiji.snt.gui.cmds

Modifier and Type	Class	Description
class	AlongPathDetectorCmd	SciJava command for detecting boutons/varicosities along traced paths using longitudinal radius and intensity profiles.
class	AnnotationGraphGeneratorCmd	SciJava Command for assembling brain annotation connectivity diagrams from tagged neurons, depicting semi-quantitative summaries of targeted brain areas.
class	BackupManagerCmd	Manages Tracing Backup files in the workspace.
class	ChooseDatasetCmd	Implements the 'Choose Tracing Image (From Open Image)...' command.
class	ColorMapReconstructionCmd	Implements Reconstruction Viewer's 'Color coding' commands.
class	ComputeSecondaryImg<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>,U extends net.imglib2.type.numeric.RealType<U> & net.imglib2.type.NativeType<U>>	Implements the "Generate Secondary Layer" command.
class	CostFunctionSelectionCmd	Entry-point command for the cost-function wizard.
class	DistributionBPCmd	Command for plotting distributions of morphometric properties (branch-related) of Trees
class	DistributionCPCmd	Command for plotting distributions of whole-cell morphometric properties of Trees
class	DuplicateCmd	GUI command for duplicating a Path.
class	FigCreatorCmd	SciJava Command for creating publication-ready figures of neuronal reconstructions in 2D and 3D formats with customizable styles and layouts.
class	FilterOrTagPathsByAngleCmd	Implements PathManagerUI's "Extension Angle(s)" prompt.
class	GraphGeneratorCmd	Command for displaying the contents of Path Manager in the "SNT Graph Viewer"
class	ImportSeedPointsCmd	Imports candidate seed points from a CSV file into SNT's SeedOverlay.
class	InsectBrainImporterCmd	Command for importing InsectBrain reconstructions
class	JSONImporterCmd	Command for importing a (MouseLight) JSON file
class	LabelProximityDetectorCmd	SciJava command for detecting proximity contacts between traced paths and labeled surfaces (segmentation images).
class	LoadReconstructionCmd	Command for loading Reconstruction files in Reconstruction Viewer.
class	LoadSeedsFromLabelsImageCmd	Generates SeedPoints from an open labels image (e.g. cellpose, Labkit, StarDist masks).
class	LoadSeedsFromROIsCmd	Generates SeedPoints from the contents of the RoiManager.
class	MLImporterCmd	Command for importing MouseLight reconstructions
class	NDFImporterCmd	Command for importing a NeuronJ NDF file.
class	OpenDatasetCmd	Implements the 'Choose Tracing Image (From File)...' command.
class	PeripathDetectorCmd	SciJava command for detecting varicosities/spines/puncta flanking traced paths.
class	RemoteSWCImporterCmd	Command for importing SWC reconstructions from remote databases
class	RestoreSessionCmd	Restores a tracing session including traces, bookmarks, and notes.
class	SaveMeasurementsCmd	Saves all open tables, plots, and charts to a specified directory.
class	SaveSessionCmd	Saves a tracing session including traces, bookmarks, notes, tables, charts, plots, and RM ROIs.
class	TranslateReconstructionsCmd	Implements Reconstruction Viewer's 'Translate...' command.
class	TwoDHistCmd	Command for plotting 2D histograms of morphometric distributions

Uses of CommonDynamicCmd in sc.fiji.snt.io

Subclasses of CommonDynamicCmd in sc.fiji.snt.io

Modifier and Type	Class	Description
class	WekaModelLoader	GUI command for Loading pre-trained models from Labkit/TWS as secondary image layer.

Uses of CommonDynamicCmd in sc.fiji.snt.plugin

Subclasses of CommonDynamicCmd in sc.fiji.snt.plugin

Modifier and Type	Class	Description
class	AnalyzerCmd	Deprecated. replaced by MeasureUI
class	AnnotationDensityCmd	Command for obtaining spine/varicosity/synapse/etc. counts from multipoint ROIs or bookmarked locations
class	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.
class	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.
class	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).
class	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.
class	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.
class	BinaryTracerCmd	Interactive command providing a GUI for BinaryTracer-based autotracing when an image is already loaded in SNT.
class	BinaryTracerCommonCmd	Abstract base command providing shared parameters and logic for BinaryTracer-based autotracing.
class	BinaryTracerFileCmd	Non-interactive command for batch BinaryTracer autotracing of all images in a directory.
class	BrainAnnotationCmd	Command to perform distribution analysis of BrainAnnotations on an annotated Tree.
class	GroupAnalyzerCmd	Command for Comparing Groups of Tree(s).
class	GrowthAnalyzerCmd	GUI command to the GrowthAnalyzer class.
class	GWDTMultiSomaCmd	Interactive command for multi-soma GWDT autotracing.
class	GWDTMultiSomaCommonCmd	Abstract base for multi-soma GWDT autotracing commands.
class	GWDTMultiSomaFileCmd	Non-interactive command for file-based multi-soma GWDT autotracing with support for single images or batch processing of a directory.
class	GWDTTracerCmd	Interactive command providing a GUI for GWDT autotracing when an image is already loaded in SNT.
class	GWDTTracerCommonCmd	Base command providing shared parameters and logic for GWDT autotracing.
class	GWDTTracerFileCmd	Non-interactive command for file-based GWDT autotracing with support for single images or batch processing of an entire directory.
class	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
class	LabkitLoaderCmd	Command for sending Path-converted ROIs to a new Labkit instance.
class	LocalThicknessCmd	Convenience command for running Fiji's "Local Thickness" plugin from SNT, enabling estimation of radii from binary skeleton images.
class	PathAnalyzerCmd	Command for measuring Paths in isolation.
class	PathMatcherCmd	Command for matching Paths across time-points (time-lapse analysis).
class	PathSpineAnalysisCmd	Command for obtaining plots pertaining to spine/varicosity counts
class	PathTimeAnalysisCmd	Command for obtaining 'time-profiles' of Paths (time-lapse analysis).
class	PlotterCmd	Implements Reconstruction Plotter, a command wrapper for interactively plotting trees using Viewer2D
class	RootAngleAnalyzerCmd	Command to perform Root angle analysis on a collection of Trees
class	ShollAnalysisBulkTreeCmd	A modified version of ShollAnalysisTreeCmd for Bulk Sholl Analysis.
class	ShollAnalysisTreeCmd	Implements SNT's commands for Sholl Analysis of Trees.
class	ShollAnalysisTreeInteractiveCmd	Interactive command for performing Sholl analysis on reconstructed neuronal tracings, with real-time parameter adjustment and interactive visualization.
class	SomaDetectorCmd	Command to automatically detect the soma (cell body) in neuronal images.
class	TreeMapperCmd	Command for color coding trees according to their properties and statistics, using MultiTreeColorMapper and TreeColorMapper.