├── .gitignore ├── LICENSE ├── PSFs └── meSPIM_PSF_kernel.mat ├── README.md ├── docs ├── Makefile ├── imgs │ ├── different_available_transforms.JPG │ ├── general_2D-to-3D_segment_figure.png │ ├── summary_figure.png │ ├── transforms_and_shape_suitability.JPG │ └── tutorials_flowchart_cheatsheet.png ├── make.bat └── source │ ├── conf.py │ ├── index.rst │ ├── modules.rst │ └── segment3D.rst ├── example_data └── .gitkeep ├── pyproject.toml ├── segment3D ├── __init__.py ├── file_io.py ├── filters.py ├── flows.py ├── gpu.py ├── meshtools.py ├── metrics.py ├── parameters.py ├── plotting.py ├── segmentation.py ├── usegment3d.py └── watershed.py ├── software ├── +cached │ ├── .TestImfinfo.m.swp │ ├── FileCache.m │ ├── FileCacheWithIndexing.m │ ├── MatFileCache.m │ ├── TestImfinfo.m │ ├── TestLoad.m │ ├── clear.m │ ├── imfinfo.m │ ├── load.m │ └── save.m ├── @BioFormatsReader │ ├── BioFormatsReader.m │ ├── getDeltaT.m │ ├── getXML.m │ └── showMetadata.m ├── @Channel │ └── Channel.m ├── @DataProcessingProcess │ └── DataProcessingProcess.m ├── @ExternalSegmentationProcess │ └── ExternalSegmentationProcess.m ├── @HCSReader │ └── HCSReader.m ├── @ImFolder │ └── ImFolder.m ├── @ImageData │ └── ImageData.m ├── @ImageDisplay │ └── ImageDisplay.m ├── @ImageOverlayDisplay │ └── ImageOverlayDisplay.m ├── @ImageProcessingProcess │ └── ImageProcessingProcess.m ├── @LineDisplay │ └── LineDisplay.m ├── @MaskProcess │ └── MaskProcess.m ├── @MovieData │ ├── MovieData.m │ ├── addAnalysisFolder.m │ ├── isequal.m │ ├── isequaln.m │ └── isequalwithequalnans.m ├── @MovieDataDisplay │ └── MovieDataDisplay.m ├── @MovieList │ ├── MovieList.m │ ├── addAnalysisFolder.m │ ├── buildByRegexp.m │ ├── minus.m │ └── plus.m ├── @MovieObject │ ├── MovieObject.m │ ├── addAnalysisFolder.m │ └── getOwnerAndProcess.m ├── @MultiScaleAutoSegmentationProcess │ └── MultiScaleAutoSegmentationProcess.m ├── @NonSingularProcess │ └── NonSingularProcess.m ├── @OmeroReader │ └── OmeroReader.m ├── @Package │ └── Package.m ├── @Process │ ├── Process.m │ └── getOwnerAndProcess.m ├── @Reader │ └── Reader.m ├── @SegmentationProcess │ └── SegmentationProcess.m ├── @TextDisplay │ └── TextDisplay.m ├── @ThresholdProcess │ └── ThresholdProcess.m ├── @ThresholdProcess3D │ └── ThresholdProcess3D.m ├── @TiffImagesReader │ └── TiffImagesReader.m ├── @TiffSeriesReader │ ├── TiffSeriesReader.m │ └── showMetadata.m ├── CellposeSegmentationProcess.m ├── CellposeSegmentationProcessGUI.fig ├── CellposeSegmentationProcessGUI.m ├── HCSplatestack.m ├── ImagePreprocessingProcess.m ├── ImagePreprocessingProcessGUI.fig ├── ImagePreprocessingProcessGUI.m ├── MakeQTMovie.m ├── PythonWrappers │ ├── segment3D_2Dto3D_aggregationMD.py │ ├── segment3D_cellpose_segmentMD.py │ ├── segment3D_enhancement_postprocessMD.py │ ├── segment3D_filtering_postprocessMD.py │ └── segment3D_preprocessMD.py ├── SegmentationEnhancementPostprocessingProcess.m ├── SegmentationEnhancementPostprocessingProcessGUI.fig ├── SegmentationEnhancementPostprocessingProcessGUI.m ├── SegmentationFilteringPostprocessingProcess.m ├── SegmentationFilteringPostprocessingProcessGUI.fig ├── SegmentationFilteringPostprocessingProcessGUI.m ├── TwoDtoThreeDAggregationProcess.m ├── TwoDtoThreeDAggregationProcessGUI.fig ├── TwoDtoThreeDAggregationProcessGUI.m ├── abstractProcessGUI.fig ├── abstractProcessGUI.m ├── addMovieViewerKeyboardShortcuts.m ├── addROIGUI.fig ├── addROIGUI.m ├── all_insequence.m ├── bfGetMemoDirectory.m ├── bfGetMemoizer.m ├── bfImport.m ├── bioformats │ ├── .nfs000000119521414d00002ee8 │ ├── NEWS.rst │ ├── bfCheckJavaMemory.m │ ├── bfCheckJavaPath.m │ ├── bfGetFileExtensions.m │ ├── bfGetPlane.m │ ├── bfGetPlaneAtZCT.m │ ├── bfGetReader.m │ ├── bfInitLogging.m │ ├── bfOpen3DVolume.m │ ├── bfTestInRange.m │ ├── bfUpgradeCheck.m │ ├── bfopen.m │ ├── bfsave.m │ ├── bioformats_package.jar │ ├── createMinimalOMEXMLMetadata.m │ └── private │ │ └── is_octave.m ├── cellposeSegmentWrap.m ├── channelGUI.fig ├── channelGUI.m ├── checkallChannels_Callback.m ├── cliGUI.m ├── cropMovie.m ├── cropMovieGUI.fig ├── cropMovieGUI.m ├── cutFirstHistMode.m ├── dataPreparationGUI.fig ├── dataPreparationGUI.m ├── deleteChannel_Callback.m ├── detectOutliers.m ├── doc │ ├── ExternalSegmentationProcess.pdf │ ├── MultiScaleAutoSegmentationProcess.pdf │ ├── SegmentationProcess.pdf │ ├── ThresholdProcess.pdf │ ├── addROIGUI.pdf │ ├── channelGUI.pdf │ ├── dataPreparationGUI.pdf │ ├── movieDataGUI.pdf │ ├── movieSelectorGUI.pdf │ └── movieViewer.pdf ├── extern │ ├── colormap_helper.m │ ├── connectOmero.m │ ├── createMask.m │ ├── createObjectDictionary.m │ ├── exportImageAsOMETIFF.m │ ├── findOmero.m │ ├── getAnnotationTypes.m │ ├── getAnnotations.m │ ├── getDatasetFileAnnotations.m │ ├── getDatasets.m │ ├── getFileAnnotationContent.m │ ├── getFileAnnotations.m │ ├── getImageFileAnnotations.m │ ├── getImages.m │ ├── getObjectAnnotations.m │ ├── getObjectTypes.m │ ├── getObjects.m │ ├── getOmeroJars.m │ ├── getProjects.m │ ├── gray.m │ ├── hsv.m │ ├── linkAnnotation.m │ ├── loadOmero.m │ ├── omeroVersion.m │ ├── rdouble.m │ ├── real2rgb.m │ ├── rescale.m │ ├── rlong.m │ ├── rstring.m │ ├── structToHashMap.m │ ├── tiffread.m │ ├── toJavaList.m │ ├── toMatlabList.m │ ├── toMatrix.m │ ├── updateFileAnnotation.m │ ├── updateOriginalFile.m │ └── writeFileAnnotation.m ├── externalSegmentationProcessGUI.fig ├── externalSegmentationProcessGUI.m ├── filterGauss2D.m ├── filterGauss3D.m ├── fsFigure.m ├── generateReport.m ├── getFilenameBody.m ├── getFilesep.m ├── getFluorPropStruct.m ├── getGaussianPSFsigma.m ├── getLCCBCopyright.m ├── getLCCBOmeroNamespace.m ├── getLensProperties.m ├── getMultiplicity.m ├── getOmeroLists.m ├── getOmeroMovies.m ├── getRelocationDirs.m ├── getindexstart.m ├── gradientFilterGauss3D.m ├── graphViewer.m ├── icon_ButtonDownFcn.m ├── icons │ ├── accepted 48 32x32.png │ ├── cancel 48 32x32.png │ ├── dialog-question-22x22.png │ ├── dialog-question-48x48.png │ ├── document-open-8.png │ └── warning 48 32x32.png ├── imDir.m ├── imFolderGUI.fig ├── imFolderGUI.m ├── imageDataGUI.fig ├── imageDataGUI.m ├── imageDataViewer.m ├── imagePreprocessWrap.m ├── importExternalData.m ├── importExternalSegmentation.m ├── inputImDPackageList.m ├── inputMLPackageList.m ├── insequence.m ├── insequence_and_scalar.m ├── intensityBinnedGradientThreshold.m ├── isConcreteClass.m ├── isProcessOrMovieData.m ├── isProcessOrMovieObject.m ├── isSubclass.m ├── isposint.m ├── isvalid.m ├── loadLCCBIcons.m ├── mex │ ├── fitGaussian2D.m │ ├── fitGaussian2D.mexa64 │ ├── fitGaussian2D.mexmaca64 │ ├── fitGaussian2D.mexmaci64 │ ├── fitGaussian2D.mexw64 │ ├── vectorialPSF.m │ ├── vectorialPSF.mexa64 │ ├── vectorialPSF.mexmaca64 │ ├── vectorialPSF.mexmaci64 │ └── vectorialPSF.mexw64 ├── mkClrDir.m ├── mkdirRobust.m ├── mockMovieData.m ├── movieDataGUI.fig ├── movieDataGUI.m ├── movieSelectorGUI.fig ├── movieSelectorGUI.m ├── movieViewer.m ├── movieViewerOptions.m ├── msaSegmentationProcessGUI.fig ├── msaSegmentationProcessGUI.m ├── msgboxGUI.fig ├── msgboxGUI.m ├── multiScaleAutoSeg_multiObject.m ├── multiscaleSeg_multiObject_2ndRun.m ├── multiscaleSeg_multiObject_im.m ├── naFromLensID.m ├── name2wavelength.m ├── noSettingsProcessGUI.fig ├── noSettingsProcessGUI.m ├── normList.m ├── omeroCacheImport.m ├── omeroDataSelectionGUI.fig ├── omeroDataSelectionGUI.m ├── omeroImport.m ├── omeroLoginGUI.fig ├── omeroLoginGUI.m ├── omeroSave.m ├── optimalHistogram.m ├── packageGUI.fig ├── packageGUI.m ├── packageGUI_OpeningFcn.m ├── packageGUI_RefreshFcn.m ├── packageGUI_RunFcn.m ├── padarrayXT.m ├── parseProcessParams.m ├── perpVector.m ├── plotScaleBar.m ├── plotTimeStamp.m ├── prepPerChannelParams.m ├── processGUI_ApplyFcn.m ├── processGUI_OpeningFcn.m ├── randomColormap.m ├── readIXMHTDFileM.m ├── readtiff.m ├── recycleProcessGUI.fig ├── recycleProcessGUI.m ├── relocatePath.m ├── runProcesses.m ├── sec2struct.m ├── segmentEnhancementPostprocessWrap.m ├── segmentFilteringPostprocessWrap.m ├── selectChannel_Callback.m ├── stackRead.m ├── stackWrite.m ├── testuSegment3DMatlabPack.m ├── threshold3DMovie.m ├── thresholdFluorescenceImage.m ├── thresholdMovie.m ├── thresholdOtsu.m ├── thresholdProcessGUI.fig ├── thresholdProcessGUI.m ├── thresholdRosin.m ├── tif3Dread.m ├── twoDtoThreeDAggregateWrap.m ├── uSegment3DPackage.m ├── uSegment3DPackageGUI.m ├── uTrackParCluster.m ├── u_quantify.m ├── userfcn_checkAllMovies.m ├── userfcn_drawIcon.m ├── userfcn_enable.m ├── userfcn_lampSwitch.m ├── userfcn_saveCheckbox.m ├── wavelength2rgb.m └── whichMatFile.m └── tutorials ├── anisotropic ├── segment_epithelial_organoid_2D_stacks.py ├── segment_epithelial_organoid_2D_stacks_with_cellpose_auto-diameter.py ├── segment_single-cell_tracking_challenge_2D_stacks.py ├── segment_single-cell_tracking_challenge_2D_stacks_with_cellpose_auto-diameter.py └── segment_unwrapped_drosophila_2D_stacks.py ├── multi_cells ├── segment_Tcells_3D.py ├── 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