| Package | Description |
|---|---|
| sc.fiji.snt.analysis |
Analysis of
Trees. |
| sc.fiji.snt.gui |
Customizations and commands for SNT's GUI.
|
| sc.fiji.snt.gui.cmds |
Scijava-based GUIs for SNT built-in commands.
|
| sc.fiji.snt.plugin |
SNT add-ons as IJ2 commands
|
| Modifier and Type | Class and Description |
|---|---|
class |
PathProfiler
Command to retrieve Profile plots (plots of voxel intensities values along a
Path) from reconstructions.
|
| Modifier and Type | Class and Description |
|---|---|
class |
SaveMeasurementsCmd
Implements the 'Save Tables and Analysis Plots...' command: A single prompt for saving all
tables, plots and charts currently open.
|
| Modifier and Type | Class and Description |
|---|---|
class |
ChooseDatasetCmd
Implements the 'Choose Tracing Image (From Open Image)...' command.
|
class |
ColorMapReconstructionCmd
Implements Reconstruction Viewer's 'Color coding' commands.
|
class |
ComputeSecondaryImg<T extends RealType<T> & NativeType<T>,U extends RealType<U> & NativeType<U>>
Implements the "Generate Secondary Layer" command.
|
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 |
GraphGeneratorCmd
Command for displaying the contents of Path Manager in the "SNT Graph Viewer"
|
class |
InsectBrainImporterCmd
Command for importing InsectBrain reconstructions
|
class |
JSONImporterCmd
Command for importing a (MouseLight) JSON file
|
class |
LoadReconstructionCmd
Command for loading Reconstruction files in Reconstruction Viewer.
|
class |
MLImporterCmd
Command for importing MouseLight reconstructions
|
class |
OpenDatasetCmd
Implements the 'Choose Tracing Image (From File)...' command.
|
class |
RemoteSWCImporterCmd
Command for importing SWC reconstructions from remote databases
|
class |
TranslateReconstructionsCmd
Implements Reconstruction Viewer's 'Translate...' command.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AnalyzerCmd
Command for measuring Tree(s).
|
class |
BrainAnnotationCmd
Command to perform distribution analysis of
BrainAnnotations on an
annotated Tree. |
class |
GroupAnalyzerCmd
Command for Comparing Groups of Tree(s).
|
class |
LocalThicknessCmd
Convenience command for running Fiji's "Local Thickness" plugin from SNT
|
class |
MultiTreeMapperCmd
Command for color coding trees according to their properties using
TreeColorMapper with options to display result in Viewer2D
and Viewer3D |
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 |
SkeletonConverterCmd
Command providing a GUI for
SkeletonConverter |
class |
SpineExtractorCmd
Command for obtaining spine/varicosity counts from multi-point ROIs
|
class |
TreeMapperCmd
Command for color coding trees according to their properties using
TreeColorMapper with options to display result in Viewer2D
and Viewer3D |
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