├── LICENSE ├── README.md ├── doc └── BlebbingCells.png └── 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 ├── @FigDisplay └── FigDisplay.m ├── @HCSReader └── HCSReader.m ├── @ImFolder └── ImFolder.m ├── @ImageAnalysisProcess └── ImageAnalysisProcess.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 ├── @NonSingularProcess └── NonSingularProcess.m ├── @OmeroReader └── OmeroReader.m ├── @Package └── Package.m ├── @Process ├── Process.m └── getOwnerAndProcess.m ├── @Reader └── Reader.m ├── @TextDisplay └── TextDisplay.m ├── @TiffImagesReader └── TiffImagesReader.m ├── @TiffSeriesReader ├── TiffSeriesReader.m └── showMetadata.m ├── Check3DCellSegmentationProcess.m ├── ComputeMIPProcess.m ├── Deconvolution3DProcess.m ├── HCSplatestack.m ├── Intensity3DProcess.m ├── Intensity3DProcessGUI.fig ├── Intensity3DProcessGUI.m ├── IntensityMotifCompare3DProcess.m ├── IntensityMotifCompare3DProcessGUI.fig ├── IntensityMotifCompare3DProcessGUI.m ├── MakeQTMovie.m ├── Mesh3DProcess.m ├── MeshMotion3DProcess.m ├── MeshMotion3DProcessGUI.fig ├── MeshMotion3DProcessGUI.m ├── MeshProcessingProcess.m ├── Morphology3DPackage.m ├── MotifDetection3DProcess.m ├── MotifDetection3DProcessGUI.fig ├── MotifDetection3DProcessGUI.m ├── PatchDescription3DProcess.m ├── PatchDescriptionForMerge3DProcess.m ├── PatchMerge3DProcess.m ├── RenderMeshProcess.m ├── RenderMeshProcessGUI.fig ├── RenderMeshProcessGUI.m ├── SurfaceSegmentation3DProcess.m ├── SurfaceSegmentation3DProcessGUI.fig ├── SurfaceSegmentation3DProcessGUI.m ├── addBlackBorder.m ├── addMovieViewerKeyboardShortcuts.m ├── addROIGUI.fig ├── addROIGUI.m ├── all_insequence.m ├── assignGradientAtNodes.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 ├── breakFaceGraph.m ├── calculateMutualVisibilityPair.m ├── calculatePairStats.m ├── calculatePairStatsOnePair.m ├── calculatePatchLength.m ├── calculateShapeDiameterFunctionRegion.m ├── calculateSmallOTF.m ├── calculateTriangleMeasurePair.m ├── cellSignalAndBackground.m ├── channelGUI.fig ├── channelGUI.m ├── checkallChannels_Callback.m ├── cliGUI.m ├── clickMeshPoints.m ├── clickOnProtrusions.m ├── closeMesh.m ├── combineImagesMeshOtsu.m ├── combineStructures.m ├── combineThreeImagesMeshOtsu.m ├── computeMIPs.m ├── computeMovieMIP.m ├── cropMovie.m ├── cropMovieGUI.fig ├── cropMovieGUI.m ├── dataPreparationGUI.fig ├── dataPreparationGUI.m ├── deconvolution3DProcessGUI.fig ├── deconvolution3DProcessGUI.m ├── deconvolveMovieMD.m ├── defaultControlParamsMorphology3DPackage.m ├── deleteChannel_Callback.m ├── depthNormalize.m ├── distanceTransformPatches.m ├── doc ├── Morphology3DPackage.pdf ├── addROIGUI.pdf ├── channelGUI.pdf ├── dataPreparationGUI.pdf ├── movieDataGUI.pdf ├── movieSelectorGUI.pdf └── movieViewer.pdf ├── estimateVonMisesFisherParameters.m ├── estimateVonMisesFisherParametersWeighted.m ├── extern ├── TriangleRayIntersection.m ├── adjacency_edge_cost_matrix.m ├── adjacency_matrix.m ├── avgedge.m ├── barycenter.m ├── bounding_box.m ├── cdt.m ├── centroid_gptbx.m ├── colormap_helper.m ├── conncomp_gptbx.m ├── connectOmero.m ├── connected_components.m ├── createMask.m ├── createObjectDictionary.m ├── doublearea.m ├── doublearea_intrinsic.m ├── edges.m ├── exportImageAsOMETIFF.m ├── findOmero.m ├── find_first_path.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 ├── in_elements.m ├── jet.m ├── linkAnnotation.m ├── loadOmero.m ├── normrow.m ├── omeroVersion.m ├── outline.m ├── path_to_libigl.m ├── path_to_tetgen.m ├── path_to_triangle.m ├── point_inside_polygon.m ├── poly2VEH.m ├── rdouble.m ├── readEDGE.m ├── readELE.m ├── readFACE.m ├── readNEIGH.m ├── readNODE.m ├── readOBJ.m ├── read_ply.m ├── real2rgb.m ├── remove_small_components.m ├── remove_unreferenced.m ├── rescale.m ├── rlong.m ├── rstring.m ├── smoothpatch.m ├── solid_angle.m ├── structToHashMap.m ├── tempprefix.m ├── tiffread.m ├── toJavaList.m ├── toMatlabList.m ├── toMatrix.m ├── triangle.m ├── triangle_triangle_adjacency.m ├── updateFileAnnotation.m ├── updateOriginalFile.m ├── upsample.m ├── vertex_neighbours.m ├── volume.m ├── winding_number.m ├── writeELE.m ├── writeFileAnnotation.m ├── writeNODE.m ├── writePOLY_tetgen.m └── writePOLY_triangle.m ├── faceColorsToVertexColorsRGB.m ├── faceNeighbors2sparse.m ├── fastIntersect.m ├── fastSetDiff.m ├── filterGauss3D.m ├── findAdjacentPatchPairs.m ├── findBoundaryFaces.m ├── findDistToRegionEdge.m ├── findEdgesFaceGraph.m ├── findInteriorMostPoint.m ├── findMeanEdgeLength.m ├── findRegionCentersFarthest.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 ├── graphOfRegion.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 ├── inputImDPackageList.m ├── inputMLPackageList.m ├── insequence.m ├── insequence_and_scalar.m ├── isConcreteClass.m ├── isSubclass.m ├── isposint.m ├── isvalid.m ├── joinWatershedLOS.m ├── joinWatershedSpillDepth.m ├── joinWatershedTriangle.m ├── joinWatershedTriangleLOS.m ├── labelWatersheds.m ├── leftRightCorrectIntensity.m ├── load3DImage.m ├── loadBlebShrunkSurfaceColor.m ├── loadBlebSurfaceColor.m ├── loadClickedOnSurfaceColor.m ├── loadCurvatureSegmentSurfaceColor.m ├── loadCurvatureSpillDepthSurfaceColor.m ├── loadCurvatureSurfaceColor.m ├── loadCurvatureWatershedsSurfaceColor.m ├── loadIntensityDepthNormalSurfaceColor.m ├── loadIntensityVertexSurfaceColor.m ├── loadLCCBIcons.m ├── loadMeshSurfaceColor.m ├── loadMotionForwardsSurfaceColor.m ├── loadMotionSurfaceColor.m ├── loadMovieData.m ├── loadProtrusionsTypeSurfaceColor.m ├── loadSVMscoreSurfaceColor.m ├── loadSVMscoreThreeSurfaceColor.m ├── loadSegmentSurfaceInterLOSColor.m ├── loadSegmentSurfaceInterTriangleColor.m ├── loadSegmentSurfacePatchMergeColor.m ├── loadSegmentSurfacePreLocalColor.m ├── make3DImageVoxelsSymmetric.m ├── makeApodizationFilter.m ├── makeColormap.m ├── makeCurvatureImage.m ├── makeDAEfile.m ├── makeGraphFromLabel.m ├── makeMeasuresMatrixForPatchMerging.m ├── makeMeasuresMatrixSVM.m ├── makeMovieDataOneChannel.m ├── makeSphere3D.m ├── makeVertices2Faces.m ├── measureAllFaceAreas.m ├── measureCellStatsStruct.m ├── measureCurvature.m ├── measureDepthOneRegion.m ├── measureDepthsAll.m ├── measureEdgeLengths.m ├── measureFaceArea.m ├── measureFacePositions.m ├── measureIntenistyVertex.m ├── measureIntensity.m ├── measureIntensityBlebCompareMeshMD.m ├── measureIntensityMeshMD.m ├── measureMeanFaceDistance.m ├── measureMeshMotionMD.m ├── measureMeshMotionNearest.m ├── measureMeshVolume.m ├── measureRegionPerimeter.m ├── measureRegionStats.m ├── measureSpherelike.m ├── measureVonMisesDiscrete.m ├── medianFilterKD.m ├── mergePatchesSVM.m ├── mergeRegionPairTriangleLOS.m ├── mesh3DProcessGUI.fig ├── mesh3DProcessGUI.m ├── meshMovieMD.m ├── meshOtsu.m ├── mex ├── KDTreeBallQuery.m ├── KDTreeBallQuery.mexa64 ├── KDTreeBallQuery.mexmaca64 ├── KDTreeBallQuery.mexmaci64 ├── KDTreeBallQuery.mexw64 ├── fitGaussian2D.m ├── fitGaussian2D.mexa64 ├── fitGaussian2D.mexmaca64 ├── fitGaussian2D.mexmaci64 ├── fitGaussian2D.mexw64 ├── kdtree_ball_query.m ├── kdtree_ball_query.mexa64 ├── kdtree_ball_query.mexmaci64 ├── kdtree_ball_query.mexw64 ├── kdtree_build.m ├── kdtree_build.mexa64 ├── kdtree_build.mexmaci64 ├── kdtree_build.mexw64 ├── kdtree_k_nearest_neighbors.m ├── kdtree_k_nearest_neighbors.mexa64 ├── kdtree_k_nearest_neighbors.mexmaci64 ├── kdtree_k_nearest_neighbors.mexw64 ├── smoothpatch_curvature_double.mexa64 ├── smoothpatch_curvature_double.mexmaci64 ├── smoothpatch_curvature_double.mexw64 ├── smoothpatch_inversedistance_double.mexa64 ├── smoothpatch_inversedistance_double.mexmaci64 ├── smoothpatch_inversedistance_double.mexw64 ├── steerableDetector3D.m ├── steerableDetector3D.mexa64 ├── steerableDetector3D.mexmaci64 ├── steerableDetector3D.mexw64 ├── vectorialPSF.m ├── vectorialPSF.mexa64 ├── vectorialPSF.mexmaca64 ├── vectorialPSF.mexmaci64 ├── vectorialPSF.mexw64 ├── vertex_neighbours_double.m ├── vertex_neighbours_double.mexa64 ├── vertex_neighbours_double.mexmaci64 └── vertex_neighbours_double.mexw64 ├── mkClrDir.m ├── mkdirRobust.m ├── mockMovieData.m ├── morphology3D.m ├── morphology3DPackageGUI.m ├── motifDetectionMeshMD.m ├── movieDataGUI.fig ├── movieDataGUI.m ├── movieSelectorGUI.fig ├── movieSelectorGUI.m ├── movieViewer.m ├── movieViewerOptions.m ├── msgboxGUI.fig ├── msgboxGUI.m ├── multiCellDetect.m ├── multiscaleSteerableFilter3D.m ├── multiscaleSurfaceFilter3D.m ├── naFromLensID.m ├── name2wavelength.m ├── noSettingsProcessGUI.fig ├── noSettingsProcessGUI.m ├── omeroCacheImport.m ├── omeroDataSelectionGUI.fig ├── omeroDataSelectionGUI.m ├── omeroImport.m ├── omeroLoginGUI.fig ├── omeroLoginGUI.m ├── omeroSave.m ├── packageGUI.fig ├── packageGUI.m ├── packageGUI_OpeningFcn.m ├── packageGUI_RefreshFcn.m ├── packageGUI_RunFcn.m ├── padarrayXT.m ├── parsave.m ├── parseProcessParams.m ├── patchDescription3DProcessGUI.fig ├── patchDescription3DProcessGUI.m ├── patchDescriptionForMergeGUI.fig ├── patchDescriptionForMergeGUI.m ├── patchDescriptionForMergeMeshMD.m ├── patchDescriptionMeshMD.m ├── patchMerge3DProcessGUI.fig ├── patchMerge3DProcessGUI.m ├── patchMergeMeshMD.m ├── plotIntensityBlebCompare.m ├── plotMeshFigure.m ├── plotMeshMD.m ├── plotMeshMDWrapper.m ├── plotScaleBar.m ├── plotTimeStamp.m ├── predictFromBlebClicks.m ├── prepPerChannelParams.m ├── prepareCellOtsuSeg.m ├── processGUI_ApplyFcn.m ├── processGUI_OpeningFcn.m ├── progressText.m ├── projMontage.m ├── randomColormap.m ├── readDAEfile.m ├── readIXMHTDFileM.m ├── readtiff.m ├── recycleProcessGUI.fig ├── recycleProcessGUI.m ├── relocatePath.m ├── removeDisconectedComponents.m ├── removeSmallWatersheds.m ├── renderMeshMD.m ├── richLucyDeconvolveFull.m ├── runDendSegment.m ├── runKrasBlebSegment.m ├── runKrasTrain.m ├── runProcesses.m ├── save3DImage.m ├── saveDAEfile.m ├── saveMeshRotation.m ├── sec2struct.m ├── segmentBlebsLOS.m ├── segmentBlebsLOSiterate.m ├── segmentBlebsLOSiterateThenLocal.m ├── segmentBlebsTriangle.m ├── selectChannel_Callback.m ├── setChannels.m ├── shrinkWatersheds.m ├── smoothDataOnMesh.m ├── splitPerChannelParams.m ├── sprintfPath.m ├── stackRead.m ├── startProcess.m ├── surface2blebStatistics.m ├── surfaceCurvatureFast.m ├── surfaceFilterGauss3D.m ├── surfaceNormalsFast.m ├── surfaceSegmentationMeshMD.m ├── svmWithFeatureSelection.m ├── threeLevelSegmentation3D.m ├── threeLevelSteerableSegmentation3D.m ├── thresholdOtsu.m ├── tif3Dread.m ├── trainProtrusionsClassifier.m ├── twoLevelSegmentation3D.m ├── uTrackParCluster.m ├── u_quantify.m ├── unpackStatisticsPairStats.m ├── userfcn_checkAllMovies.m ├── userfcn_drawIcon.m ├── userfcn_enable.m ├── userfcn_lampSwitch.m ├── userfcn_saveCheckbox.m ├── validateBlebClassifier.m ├── wavelength2rgb.m ├── weinerDeconvolve.m ├── weinerDeconvolveFull.m └── whichMatFile.m /LICENSE: -------------------------------------------------------------------------------- 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