Package sc.fiji.snt.gui.cmds

package sc.fiji.snt.gui.cmds

Scijava-based GUIs for SNT built-in commands. There should not be a need to script these directly. However, the source code of these simple Commands exemplifies how to script SNTService

Author:

Tiago Ferreira

Related Packages

Package	Description
sc.fiji.snt.gui	Customizations and commands for SNT's GUI.

Classes

Class	Description
AddTextAnnotationCmd	Implements Reconstruction Viewer's 'Add Annotation Label...' commands.
AlongPathDetectorCmd	SciJava command for detecting boutons/varicosities along traced paths using longitudinal radius and intensity profiles.
AnnotationGraphGeneratorCmd	SciJava Command for assembling brain annotation connectivity diagrams from tagged neurons, depicting semi-quantitative summaries of targeted brain areas.
AnnotationGraphRecViewerCmd	SciJava Command for displaying annotation graph data in the Reconstruction Viewer with customizable color metrics and mesh opacity.
AutoTraceConfigDialog	Non-modal dialog displaying AutoTraceConfig results in a JTable with checkboxes, allowing the user to cherry-pick which derived parameters to apply.
BackupManagerCmd	Manages Tracing Backup files in the workspace.
BvvCmd	Convenience command for starting a standalone Bvv instance.
BvvRenderingOptionsCmd	Command providing a GUI for configuring Bvv.PathRenderingOptions.
ChooseDatasetCmd	Implements the 'Choose Tracing Image (From Open Image)...' command.
ColorMapReconstructionCmd	Implements Reconstruction Viewer's 'Color coding' commands.
CommonDynamicCmd	Command class for GUI commands extending DynamicCommand
CompareFilesCmd	Command for opening two SWC/traces files in a dedicated Reconstruction Viewer.
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.
CostFunctionSelectionCmd	Entry-point command for the cost-function wizard.
CustomizeAxesCmd	Command for customizing axis-to-anatomy mappings in Reconstruction Viewer.
CustomizeLegendCmd	Command for customizing a LUT legend in Reconstruction Viewer
CustomizeObjCmd	Command for customizing an OBJ mesh in Reconstruction Viewer
CustomizeTreeCmd	Command for customizing selected Trees in Reconstruction Viewer.
DistributionBPCmd	Command for plotting distributions of morphometric properties (branch-related) of Trees
DistributionCPCmd	Command for plotting distributions of whole-cell morphometric properties of Trees
DuplicateCmd	GUI command for duplicating a Path.
EnableSciViewUpdateSiteCmd	Implements the 'EnableSciViewUpdateSite' command.
FigCreatorCmd	SciJava Command for creating publication-ready figures of neuronal reconstructions in 2D and 3D formats with customizable styles and layouts.
FilterOrTagPathsByAngleCmd	Implements PathManagerUI's "Extension Angle(s)" prompt.
GraphGeneratorCmd	Command for displaying the contents of Path Manager in the "SNT Graph Viewer"
ImportSeedPointsCmd	Imports candidate seed points from a CSV file into SNT's SeedOverlay.
InsectBrainImporterCmd	Command for importing InsectBrain reconstructions
JSONImporterCmd	Command for importing a (MouseLight) JSON file
LabelProximityDetectorCmd	SciJava command for detecting proximity contacts between traced paths and labeled surfaces (segmentation images).
LoadObjCmd	Command for loading an OBJ file in Reconstruction Viewer
LoadReconstructionCmd	Command for loading Reconstruction files in Reconstruction Viewer.
LoadSeedsFromLabelsImageCmd	Generates SeedPoints from an open labels image (e.g. cellpose, Labkit, StarDist masks).
LoadSeedsFromROIsCmd	Generates SeedPoints from the contents of the RoiManager.
MLImporterCmd	Command for importing MouseLight reconstructions
MultiSpectralRefinerCmd	GUI command for MultiSpectralRefiner.
MultiSWCImporterCmd	Command for importing a folder of SWC files.
mxCircleLayoutGroupedCmd	SciJava Command implementing grouped circular layout algorithm for graph visualization with multi-level organizational hierarchy support.
mxOrganicLayoutPrefsCmd	Command for setting parameters of the mxOrganicLayout Graph layout used in GraphEditor.
NDFImporterCmd	Command for importing a NeuronJ NDF file.
NewGraphOptionsCmd	GUI for "New Graph Options" Command
OpenDatasetCmd	Implements the 'Choose Tracing Image (From File)...' command.
PathFitterCmd	GUI command for PathFitter
PeripathDetectorCmd	SciJava command for detecting varicosities/spines/puncta flanking traced paths.
PersistenceAnalyzerCmd	GUI command persistent homology analyses.
PrefsCmd	Command for (re)setting SNT Preferences.
ReconstructionViewerCmd	Command for starting Reconstruction Viewer as a 'stand-alone' program
RecViewerPrefsCmd	Command implementing Reconstruction Viewer 'Preferences...' command.
RemoteSWCImporterCmd	Command for importing SWC reconstructions from remote databases
RestoreSessionCmd	Restores a tracing session including traces, bookmarks, and notes.
SaveMeasurementsCmd	Saves all open tables, plots, and charts to a specified directory.
SaveSessionCmd	Saves a tracing session including traces, bookmarks, notes, tables, charts, plots, and RM ROIs.
ShortcutWindowCmd	A command that displays a shortcut window of most popular commands, inspired by the Bio-Formats Plugins Shortcut Window.
ShowCorrespondencesCmd	Command for highlighting the correspondences between two reconstructions in the Legacy 3D Viewer
SNTLoaderCmd	Command for Launching SNT
SpotSpineLoaderCmd	Implements the 'Open Spot Spine...' command.
SWCTypeFilterCmd	Implements PathManagerUI's SWC-type filtering Command.
SWCTypeOptionsCmd	Implements PathManagerUI's SWC-SWC-type tagging Options Command.
TranslateReconstructionsCmd	Implements Reconstruction Viewer's 'Translate...' command.
TreeGraphRecViewerCmd	SciJava Command for displaying tree graph structures in the Reconstruction Viewer as interactive 3D visualizations.
TwoDHistCmd	Command for plotting 2D histograms of morphometric distributions