├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── config.yml │ ├── documentation.md │ └── feature_request.md ├── build.sh ├── dependabot.yml ├── setup.sh └── workflows │ ├── build.yml │ └── codeql-analysis.yml ├── .gitignore ├── .gitignore.master ├── .gitpod.dockerfile ├── .gitpod.yml ├── .settings └── org.eclipse.jdt.core.prefs ├── CITATION.cff ├── LICENSE.txt ├── NOTES.md ├── README.md ├── docs └── index.html ├── macros ├── AutoRun │ └── AutoRun_SNT_Tool.ijm └── toolsets │ └── Neuroanatomy Shortcuts.ijm ├── notebooks └── README.md ├── pom.xml └── src ├── main ├── java │ └── sc │ │ └── fiji │ │ └── snt │ │ ├── BookmarkManager.java │ │ ├── ClarifyingKeyListener.java │ │ ├── DelineationsManager.java │ │ ├── Fill.java │ │ ├── FillConverter.java │ │ ├── FillManagerUI.java │ │ ├── FillerProgressCallback.java │ │ ├── FittingProgress.java │ │ ├── HessianGenerationCallback.java │ │ ├── InteractiveTracerCanvas.java │ │ ├── MultiTaskProgress.java │ │ ├── NearPoint.java │ │ ├── NormalPlaneCanvas.java │ │ ├── NotesUI.java │ │ ├── Path.java │ │ ├── PathAndFillListener.java │ │ ├── PathAndFillManager.java │ │ ├── PathChangeEvent.java │ │ ├── PathChangeListener.java │ │ ├── PathDownsampler.java │ │ ├── PathFitter.java │ │ ├── PathManagerUI.java │ │ ├── PathNodeCanvas.java │ │ ├── PathTransformer.java │ │ ├── QueueJumpingKeyListener.java │ │ ├── SNT.java │ │ ├── SNTPrefs.java │ │ ├── SNTService.java │ │ ├── SNTUI.java │ │ ├── SNTUtils.java │ │ ├── SciViewSNT.java │ │ ├── SearchProgressCallback.java │ │ ├── TracerCanvas.java │ │ ├── Tree.java │ │ ├── TreeProperties.java │ │ ├── analysis │ │ ├── AbstractConvexHull.java │ │ ├── AnalysisUtils.java │ │ ├── AnnotationMapper.java │ │ ├── CircularModels.java │ │ ├── ColorMapper.java │ │ ├── ConvexHull2D.java │ │ ├── ConvexHull3D.java │ │ ├── ConvexHullAnalyzer.java │ │ ├── GroupedTreeStatistics.java │ │ ├── MultiTreeColorMapper.java │ │ ├── MultiTreeStatistics.java │ │ ├── NodeColorMapper.java │ │ ├── NodeProfiler.java │ │ ├── NodeStatistics.java │ │ ├── PCAnalyzer.java │ │ ├── PathProfiler.java │ │ ├── PathStatistics.java │ │ ├── PathStraightener.java │ │ ├── PersistenceAnalyzer.java │ │ ├── ProfileProcessor.java │ │ ├── RoiConverter.java │ │ ├── RootAngleAnalyzer.java │ │ ├── SNTChart.java │ │ ├── SNTTable.java │ │ ├── ShollAnalyzer.java │ │ ├── SkeletonConverter.java │ │ ├── StrahlerAnalyzer.java │ │ ├── TreeAnalyzer.java │ │ ├── TreeColorMapper.java │ │ ├── TreeStatistics.java │ │ ├── UnknownMetricException.java │ │ ├── graph │ │ │ ├── AnnotationGraph.java │ │ │ ├── AnnotationGraphUtils.java │ │ │ ├── AnnotationWeightedEdge.java │ │ │ ├── DirectedWeightedGraph.java │ │ │ ├── DirectedWeightedSubgraph.java │ │ │ ├── GraphColorMapper.java │ │ │ ├── GraphUtils.java │ │ │ ├── SNTGraph.java │ │ │ ├── SNTPseudograph.java │ │ │ ├── SWCWeightedEdge.java │ │ │ └── package-info.java │ │ ├── growth │ │ │ ├── GrowthAnalysisResults.java │ │ │ ├── GrowthAnalyzer.java │ │ │ ├── NeuriteGrowthData.java │ │ │ └── package-info.java │ │ ├── package-info.java │ │ └── sholl │ │ │ ├── Profile.java │ │ │ ├── ProfileEntry.java │ │ │ ├── ProfileProperties.java │ │ │ ├── ShollUtils.java │ │ │ ├── gui │ │ │ ├── ShollOverlay.java │ │ │ ├── ShollPlot.java │ │ │ ├── ShollTable.java │ │ │ └── package-info.java │ │ │ ├── math │ │ │ ├── CommonStats.java │ │ │ ├── Comparator.java │ │ │ ├── LinearProfileStats.java │ │ │ ├── NormalizedProfileStats.java │ │ │ ├── PolarProfileStats.java │ │ │ ├── ShollStats.java │ │ │ └── package-info.java │ │ │ ├── package-info.java │ │ │ └── parsers │ │ │ ├── ImageParser.java │ │ │ ├── ImageParser2D.java │ │ │ ├── ImageParser3D.java │ │ │ ├── Parser.java │ │ │ ├── TabularParser.java │ │ │ ├── TreeParser.java │ │ │ └── package-info.java │ │ ├── annotation │ │ ├── AllenCompartment.java │ │ ├── AllenUtils.java │ │ ├── BrainAnnotation.java │ │ ├── InsectBrainCompartment.java │ │ ├── InsectBrainUtils.java │ │ ├── VFBUtils.java │ │ ├── ZBAtlasUtils.java │ │ └── package-info.java │ │ ├── event │ │ ├── SNTEvent.java │ │ ├── SNTListener.java │ │ └── package-info.java │ │ ├── filter │ │ ├── Frangi.java │ │ ├── Lazy.java │ │ ├── Tubeness.java │ │ ├── UnaryComputerOpCellLoader.java │ │ └── package-info.java │ │ ├── gui │ │ ├── CheckboxSpinner.java │ │ ├── CollapsiblePanel.java │ │ ├── ColorChangedListener.java │ │ ├── ColorChooserButton.java │ │ ├── ColorMenu.java │ │ ├── ComponentMover.java │ │ ├── ComponentResizer.java │ │ ├── DemoRunner.java │ │ ├── EnhancedGenericDialog.java │ │ ├── FADerivedIcon.java │ │ ├── FileChooser.java │ │ ├── FileDrop.java │ │ ├── FilePicker.java │ │ ├── GuiUtils.java │ │ ├── IconFactory.java │ │ ├── MeasureUI.java │ │ ├── PathManagerUISearchableBar.java │ │ ├── SNTCommandFinder.java │ │ ├── SNTEditorPane.java │ │ ├── SNTREPL.java │ │ ├── SNTSearchableBar.java │ │ ├── SWCExportDialog.java │ │ ├── SWCImportDialog.java │ │ ├── SaveMeasurementsCmd.java │ │ ├── ScriptInstaller.java │ │ ├── ScriptRecorder.java │ │ ├── SearchField.java │ │ ├── SigmaPalette.java │ │ ├── SigmaPaletteListener.java │ │ ├── SplashScreen.java │ │ ├── SwingSafeResult.java │ │ ├── cmds │ │ │ ├── AddTextAnnotationCmd.java │ │ │ ├── AnnotationGraphGeneratorCmd.java │ │ │ ├── AnnotationGraphRecViewerCmd.java │ │ │ ├── ChooseDatasetCmd.java │ │ │ ├── ColorMapReconstructionCmd.java │ │ │ ├── CommonDynamicCmd.java │ │ │ ├── CompareFilesCmd.java │ │ │ ├── ComputeSecondaryImg.java │ │ │ ├── CustomizeLegendCmd.java │ │ │ ├── CustomizeObjCmd.java │ │ │ ├── CustomizeTreeCmd.java │ │ │ ├── DistributionBPCmd.java │ │ │ ├── DistributionCPCmd.java │ │ │ ├── DuplicateCmd.java │ │ │ ├── EnableSciViewUpdateSiteCmd.java │ │ │ ├── FigCreatorCmd.java │ │ │ ├── FilterOrTagPathsByAngleCmd.java │ │ │ ├── GraphGeneratorCmd.java │ │ │ ├── InsectBrainImporterCmd.java │ │ │ ├── JSONImporterCmd.java │ │ │ ├── LoadObjCmd.java │ │ │ ├── LoadReconstructionCmd.java │ │ │ ├── MLImporterCmd.java │ │ │ ├── MultiSWCImporterCmd.java │ │ │ ├── NDFImporterCmd.java │ │ │ ├── NewGraphOptionsCmd.java │ │ │ ├── OpenDatasetCmd.java │ │ │ ├── PathFitterCmd.java │ │ │ ├── PersistenceAnalyzerCmd.java │ │ │ ├── PrefsCmd.java │ │ │ ├── RecViewerPrefsCmd.java │ │ │ ├── ReconstructionViewerCmd.java │ │ │ ├── RemoteSWCImporterCmd.java │ │ │ ├── SNTLoaderCmd.java │ │ │ ├── SWCTypeFilterCmd.java │ │ │ ├── SWCTypeOptionsCmd.java │ │ │ ├── ShortcutWindowCmd.java │ │ │ ├── ShowCorrespondencesCmd.java │ │ │ ├── SpotSpineLoaderCmd.java │ │ │ ├── TranslateReconstructionsCmd.java │ │ │ ├── TreeGraphRecViewerCmd.java │ │ │ ├── TwoDHistCmd.java │ │ │ ├── mxCircleLayoutGroupedCmd.java │ │ │ ├── mxOrganicLayoutPrefsCmd.java │ │ │ └── package-info.java │ │ └── package-info.java │ │ ├── hyperpanes │ │ ├── MultiDThreePanes.java │ │ ├── MultiDThreePanesCanvas.java │ │ ├── PaneOwner.java │ │ └── package-info.java │ │ ├── io │ │ ├── FlyCircuitLoader.java │ │ ├── InsectBrainLoader.java │ │ ├── MouseLightLoader.java │ │ ├── MouseLightQuerier.java │ │ ├── NDFImporter.java │ │ ├── NeuroMorphoLoader.java │ │ ├── RemoteSWCLoader.java │ │ ├── SWCExportException.java │ │ ├── TracesFileFormatException.java │ │ ├── WekaModelLoader.java │ │ └── package-info.java │ │ ├── package-info.java │ │ ├── plugin │ │ ├── AnalyzerCmd.java │ │ ├── BrainAnnotationCmd.java │ │ ├── ChooseDataset.java │ │ ├── ConvexHullCmd.java │ │ ├── GraphAdapterMapperCmd.java │ │ ├── GroupAnalyzerCmd.java │ │ ├── GrowthAnalyzerCmd.java │ │ ├── InterpolateRadiiCmd.java │ │ ├── LabkitLoaderCmd.java │ │ ├── LocalThicknessCmd.java │ │ ├── PathAnalyzerCmd.java │ │ ├── PathMatcherCmd.java │ │ ├── PathOrderAnalysisCmd.java │ │ ├── PathSpineAnalysisCmd.java │ │ ├── PathTimeAnalysisCmd.java │ │ ├── PlotterCmd.java │ │ ├── ROIExporterCmd.java │ │ ├── RootAngleAnalyzerCmd.java │ │ ├── ShollAnalysisBulkTreeCmd.java │ │ ├── ShollAnalysisImgCmd.java │ │ ├── ShollAnalysisImgCommonCmd.java │ │ ├── ShollAnalysisImgInteractiveCmd.java │ │ ├── ShollAnalysisPrefsCmd.java │ │ ├── ShollAnalysisTreeCmd.java │ │ ├── ShollAnalysisTreeInteractiveCmd.java │ │ ├── SkeletonConverterCmd.java │ │ ├── SkeletonizerCmd.java │ │ ├── SpineExtractorCmd.java │ │ ├── StrahlerCmd.java │ │ ├── TWSLoaderCmd.java │ │ ├── TreeMapperCmd.java │ │ ├── ij1 │ │ │ ├── Strahler.java │ │ │ ├── SummarizeSkeleton.java │ │ │ └── package-info.java │ │ └── package-info.java │ │ ├── tracing │ │ ├── AbstractSearch.java │ │ ├── BiSearch.java │ │ ├── BiSearchNode.java │ │ ├── DefaultSearchNode.java │ │ ├── FillerThread.java │ │ ├── ManualTracerThread.java │ │ ├── PathResult.java │ │ ├── SearchInterface.java │ │ ├── SearchNode.java │ │ ├── SearchThread.java │ │ ├── TracerThread.java │ │ ├── TubularGeodesicsTracer.java │ │ ├── artist │ │ │ ├── BiSearchArtist.java │ │ │ ├── FillerThreadArtist.java │ │ │ ├── SearchArtist.java │ │ │ ├── SearchArtistFactory.java │ │ │ ├── SearchThreadArtist.java │ │ │ └── package-info.java │ │ ├── cost │ │ │ ├── Cost.java │ │ │ ├── Difference.java │ │ │ ├── DifferenceSq.java │ │ │ ├── OneMinusErf.java │ │ │ ├── Reciprocal.java │ │ │ └── package-info.java │ │ ├── heuristic │ │ │ ├── Dijkstra.java │ │ │ ├── Euclidean.java │ │ │ ├── Heuristic.java │ │ │ └── package-info.java │ │ ├── image │ │ │ ├── ArraySearchImage.java │ │ │ ├── ListSearchImage.java │ │ │ ├── MapSearchImage.java │ │ │ ├── SearchImage.java │ │ │ ├── SearchImageStack.java │ │ │ ├── SupplierUtil.java │ │ │ └── package-info.java │ │ └── package-info.java │ │ ├── util │ │ ├── BoundingBox.java │ │ ├── CircleCursor3D.java │ │ ├── ColorMaps.java │ │ ├── CrossoverFinder.java │ │ ├── DiskCursor3D.java │ │ ├── ImgUtils.java │ │ ├── ImpUtils.java │ │ ├── LSystemsTree.java │ │ ├── LinAlgUtils.java │ │ ├── Logger.java │ │ ├── PathCursor.java │ │ ├── PointInCanvas.java │ │ ├── PointInImage.java │ │ ├── SNTColor.java │ │ ├── SNTPoint.java │ │ ├── SWCPoint.java │ │ ├── ShollPoint.java │ │ ├── SigmaUtils.java │ │ └── package-info.java │ │ └── viewer │ │ ├── Annotation3D.java │ │ ├── Bvv.java │ │ ├── ColorTableMapper.java │ │ ├── GraphViewer.java │ │ ├── MaterialEditor.java │ │ ├── MultiViewer2D.java │ │ ├── MultiViewer3D.java │ │ ├── OBJMesh.java │ │ ├── Viewer2D.java │ │ ├── Viewer3D.java │ │ ├── geditor │ │ ├── AnnotationGraphAdapter.java │ │ ├── AnnotationGraphComponent.java │ │ ├── DefaultFileFilter.java │ │ ├── EditorActions.java │ │ ├── EditorConsole.java │ │ ├── EditorKeyboardHandler.java │ │ ├── EditorMenuBar.java │ │ ├── EditorPopupMenu.java │ │ ├── EditorRuler.java │ │ ├── EditorToolBar.java │ │ ├── GraphConfigDialog.java │ │ ├── GraphEditor.java │ │ ├── SNTGraphAdapter.java │ │ ├── SNTGraphComponent.java │ │ ├── SNTPseudographAdapter.java │ │ ├── SNTPseudographComponent.java │ │ ├── TextAreaOutputStream.java │ │ ├── TreeGraphAdapter.java │ │ ├── TreeGraphComponent.java │ │ ├── mxCircleLayoutGrouped.java │ │ ├── mxCircleLayoutScaled.java │ │ ├── mxCircleLayoutSorted.java │ │ └── package-info.java │ │ └── package-info.java └── resources │ ├── geditor │ ├── default-style.xml │ ├── editor.properties │ ├── formal-style-dark.xml │ ├── formal-style.xml │ ├── minimal-style.xml │ └── shapes.xml │ ├── logback.xml │ ├── meshes │ ├── FCWB.obj │ ├── JFRCtemplate2010.obj │ ├── JFRCtemplate2013.obj │ ├── JFRCtemplate2018.obj │ ├── MouseBrainAllen2.5.obj │ ├── MouseBrainAllen3.obj │ └── ZfKunst2019.obj │ ├── misc │ └── SNTLogo512x528.png │ ├── ml │ ├── brainAreas_v2.5.json │ ├── brainAreas_v3.json │ ├── demo-trees │ │ ├── AA0001-4.json │ │ ├── AA0001.swc │ │ ├── AA0002.swc │ │ ├── AA0003.swc │ │ └── AA0004.swc │ ├── structureIdentifiers.json │ └── tracingStructures.json │ ├── plugins.config │ ├── script_templates │ └── Neuroanatomy │ │ ├── Analysis │ │ ├── Analysis_Demo.py │ │ ├── Analysis_Demo_(Interactive).py │ │ ├── Brain_Compartment_Analysis_Demo.py │ │ ├── Branch_Angles_vs_Distance_To_Soma.py │ │ ├── Compare_Cell_Groups.groovy │ │ ├── Draw_Disks_Demo.groovy │ │ ├── Flow_and_Ferris-Wheel_Diagrams_Demo.groovy │ │ ├── Get_Branch_Points_in_Brain_Compartment_Demo.groovy │ │ ├── Graph_Analysis_Demo.py │ │ ├── Root_Angle_Analysis.groovy │ │ ├── Sholl_Bitmap_vs_Tracing_Comparison.groovy │ │ ├── Sholl_Convex_Hull_As_Center.groovy │ │ ├── Sholl_Extensive_Stats_Demo.groovy │ │ ├── Sholl_Extract_Profile_From_Image_Demo.py │ │ ├── Sholl_Merge_Grouped_Profiles.py │ │ ├── Sholl_Rasterize_Shells.py │ │ ├── Strahler_Analysis.py │ │ ├── Tree_Mesh_Direction_Analysis.groovy │ │ ├── Tree_Span_Angle_Analysis.groovy │ │ └── Two_Dimensional_Histogram_Demo.py │ │ ├── Batch │ │ ├── Convert_NeuronJ_Tracings_to_ROIs.py │ │ ├── Convert_Traces_to_SWC.py │ │ ├── Convex_Hull_Bulk_Analysis.py │ │ ├── Download_ML_Data_(Demo_I).groovy │ │ ├── Download_ML_Data_(Demo_II).scala │ │ ├── Filter_Multiple_Images.py │ │ ├── Measure_Multiple_Files.py │ │ ├── Measure_Multiple_Files_(With_Options).groovy │ │ ├── Sholl_Bulk_Analysis_(From_Reconstructions).groovy │ │ └── Strahler_Bulk_Analysis_(From_Reconstructions).py │ │ ├── Boilerplate │ │ ├── BSH.bsh │ │ ├── GVY.groovy │ │ └── PY.py │ │ ├── Misc │ │ ├── Monitor_Memory.groovy │ │ └── Set_A_Timer_.groovy │ │ ├── Render │ │ ├── Reconstruction_Viewer_Demo.py │ │ ├── Reconstruction_Viewer_Headless_Demo.groovy │ │ ├── Render_Cell_Collection_2D_(MultiPanel_Figure).groovy │ │ ├── Render_Cell_Collection_2D_(Skeletonized_Montage).groovy │ │ ├── Render_Cell_Collection_3D.groovy │ │ ├── Render_ML_somata.groovy │ │ └── Sciview_Demo.groovy │ │ ├── Skeletons_and_ROIs │ │ ├── Classify_Particles_Using_Skeleton.py │ │ ├── Convert_Reconstruction_To_ROIs.groovy │ │ ├── Delaunay_Triangulation.groovy │ │ ├── Density_Map.py │ │ ├── Gaussian_Density_Map.py │ │ ├── Reconstruction_From_Segmented_Image.py │ │ └── Straightening_Montage.groovy │ │ ├── Time-lapses │ │ └── Apply_3D_Drift_Corrections.py │ │ └── Tracing │ │ ├── Apply_Weka_Model_To_Tracing_Image.groovy │ │ ├── Fill_Demo.py │ │ ├── Fully_Automated_Tracing_Demo_(Interactive).py │ │ ├── Fully_Automated_Tracing_Timelapse_Demo.groovy │ │ ├── Path_Player.py │ │ ├── Scripted_Tracing_Demo.py │ │ ├── Scripted_Tracing_Demo_(Interactive).py │ │ ├── Set_CT_Position_Of_Selected_Paths.groovy │ │ ├── Take_Snapshot.py │ │ ├── Take_Snapshot_(Traces_Only).py │ │ ├── Train_Weka_Classifier.groovy │ │ └── Transform_Paths.py │ └── tests │ ├── 21dpi_contra_infra_01.swc │ ├── OP_1-gs.swc │ ├── TreeV.swc │ ├── TreeV.tif │ ├── TreeVsimplified.swc │ ├── ddaC.tif │ ├── ddaC_info │ └── ddaCsample.csv └── test ├── java └── sc │ └── fiji │ └── snt │ ├── IOTest.java │ ├── MLTreeTest.java │ ├── PathConnectivityTest.java │ ├── PathExtensionAngleTest.java │ ├── PersistenceAnalyzerTest.java │ ├── ScriptTemplatesTest.java │ ├── SkeletonConverterTest.java │ ├── Tracing2DTest.java │ ├── Tracing3DTest.java │ ├── TreeSkeletonTest.java │ ├── TreeStatisticsATest.java │ ├── TreeStatisticsBTest.java │ ├── analysis │ ├── PCAnalyzerTest.java │ └── graph │ │ └── DirectedWeightedGraphTest.java │ ├── annotation │ ├── AllenCompartmentTest.java │ └── AllenUtilsTest.java │ ├── demo │ ├── RecViewerDemo.java │ ├── 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