├── .gitignore ├── Analysis ├── AddCaption.m ├── AxesStyles │ ├── ApplyStyle.m │ ├── FormatFigure.m │ ├── NoStyle.m │ ├── PrintStyle.m │ ├── PublicationStyle.m │ └── ScreenStyle.m ├── CellAnalysis │ ├── Plot_AllTrajectories.m │ ├── Plot_AxisRatio.m │ ├── Plot_CellCount.m │ ├── Plot_CellSize.m │ ├── Plot_Fluorescence.m │ ├── Plot_LineageTree.m │ ├── Plot_ParameterTree.m │ ├── Plot_TotalDistance.m │ ├── Tree_AvgAxisRatio.m │ ├── Tree_AvgSize.m │ ├── Tree_AvgSpeed.m │ └── Trees.m ├── Fibers │ ├── CentralNuclei.m │ ├── FiberAnalysis.m │ └── IsCellOnBorder.m ├── FusionIndex │ └── FusionIndex.m ├── GetLabel.m ├── GetTitle.m ├── Plots │ ├── AgeHistogram.m │ ├── AxisRatioOverTime.m │ ├── CellAge.m │ ├── CloneSize.m │ ├── CloneViability.m │ ├── DeadCellRatio.m │ ├── DeadCount.m │ ├── DivisionCount.m │ ├── FateProbabilityGeneration.m │ ├── GenerationDistribution.m │ ├── LiveCount.m │ ├── LiveDead.m │ ├── LiveDeadGhost.m │ ├── OverTime_generic.m │ ├── PlotFigure.m │ ├── PlotGUI.m │ ├── ProliferationProfile.m │ ├── SizeOverTime.m │ ├── SpeedOverTime.m │ └── SurvivingCount.m ├── Plotting │ ├── Cells │ │ ├── PlotApoptosis.m │ │ ├── PlotAppearance.m │ │ ├── PlotDisappearance.m │ │ ├── PlotMitosis.m │ │ ├── PlotOutlines.m │ │ └── PlotTrajectories.m │ ├── GetBoundaries.m │ ├── PlotFilled.m │ ├── PlotWithNan.m │ ├── ScatterPlot.m │ └── SetYLimits.m └── PopulationAnalysis │ ├── CDF.m │ ├── Histogram.m │ ├── KernelSmoothingDensity.m │ ├── MultiAxFig.m │ ├── OverTime.m │ ├── ParentVsAllChildren.m │ ├── ParentVsChildren.m │ ├── PlotConditionProperty.m │ ├── Scatter.m │ ├── ScatterPlotGUI.m │ ├── SingleAxFig.m │ ├── Sorted.m │ └── Symmetry.m ├── AnalysisExample.m ├── BaxterAlgorithms.m ├── BaxterAlgorithms.prj ├── BaxterAlgorithmsTermial.m ├── BaxterAlgorithms_resources ├── icon.ico ├── icon_16.png ├── icon_24.png ├── icon_32.png └── icon_48.png ├── Blob ├── AxisLengths2.m ├── AxisLengths3.m ├── Blob.m ├── Brush │ ├── Brush.m │ ├── Brush3D.m │ ├── ConvexDisk.m │ └── ConvexEllipse.m ├── CropBlobs.m ├── IndexBlobs.m ├── Labels2Blobs.m ├── MorphOperators │ ├── BlobMorphOp.m │ ├── BwConvHull3D.m │ ├── CloseAllBlobs.m │ ├── CloseBlob.m │ ├── CombineBlobs.m │ ├── CombineBlobs3D.m │ ├── ConvexAllBlobs.m │ ├── ConvexBlob.m │ ├── CropBlobZeros.m │ ├── DilateBlob.m │ ├── DilateBlob3D.m │ ├── OpenAllBlobs.m │ ├── OpenBlob.m │ └── RemoveBlobPixels.m ├── MoveBlobCentroids.m ├── Overlap.m ├── PixelPerimeter.m ├── ReconstructSegmentsBlob.m ├── RemovePointBlobs.m └── SortBlobs.m ├── Cell ├── AliveCells.m ├── AreCells.m ├── Cell.m ├── Cells2Blobs.m ├── ClearCellNotes.m ├── ColorCells.m ├── ColorLineageTree.m ├── ComputeRegionPropsCells.m ├── CopyCellVec.m ├── CountCells.m ├── CropCells.m ├── ErodeFOI.m ├── ExportCellsTif.m ├── ExtractProperty.m ├── GetProperties.m ├── LoadCells.m ├── LoadCellsTif.m ├── MoveCentroids.m ├── NotCells.m ├── PartitionCells.m ├── PointSegmentCells.m ├── ReconstructSegments.m ├── RemoveOutlines.m ├── SaveCells.m ├── SaveCellsTif.m ├── SaveCellsXML.m ├── SaveSEGGT.m ├── SaveSelected │ ├── AvgMinPixelDist.m │ ├── GetGTBlobs.m │ ├── KalmanFilterCell.m │ ├── SaveSelectedGTCells.m │ └── SelectCellsFromGTPixels.m ├── SaveTRAGT.m ├── SetdiffCells.m ├── SortCells.m ├── SortClones.m ├── TimeSpan.m ├── TrimCells.m └── UniqueCells.m ├── CompileMex.m ├── External ├── ParforProgMonv2 │ ├── ParforProgMon.m │ ├── example.m │ ├── java │ │ ├── ParforProgressMonitor$1.class │ │ ├── ParforProgressMonitor$ProgServer$1.class │ │ ├── ParforProgressMonitor$ProgServer.class │ │ ├── ParforProgressMonitor$ProgThing.class │ │ ├── ParforProgressMonitor$ProgWorker.class │ │ ├── ParforProgressMonitor.class │ │ └── ParforProgressMonitor.java │ └── license.txt ├── bwdistsc │ ├── bwdistsc.m │ └── license.txt ├── getGitInfo │ ├── getGitInfo.m │ └── license.txt ├── medfilt3 │ ├── license.txt │ └── medfilt3.m ├── plotboxpos │ ├── LICENSE.txt │ └── plotboxpos.m └── uigetfile_n_dir │ ├── UiGetMultipleDirs.m │ └── license.txt ├── Files ├── Classifiers │ ├── Count │ │ ├── CTC2015 │ │ │ └── Fluo-N3DL-DRO_01_cropped_weight_GT.mat │ │ ├── ISBI2015 │ │ │ ├── MICROTUBULE snr 1 density high_weight.mat │ │ │ ├── MICROTUBULE snr 1 density low_weight.mat │ │ │ ├── MICROTUBULE snr 1 density mid_weight.mat │ │ │ ├── MICROTUBULE snr 2 density high_weight.mat │ │ │ ├── MICROTUBULE snr 2 density low_weight.mat │ │ │ ├── MICROTUBULE snr 2 density mid_weight.mat │ │ │ ├── MICROTUBULE snr 4 density high_weight.mat │ │ │ ├── MICROTUBULE snr 4 density low_weight.mat │ │ │ ├── MICROTUBULE snr 4 density mid_weight.mat │ │ │ ├── MICROTUBULE snr 7 density high_weight.mat │ │ │ ├── MICROTUBULE snr 7 density low_weight.mat │ │ │ ├── MICROTUBULE snr 7 density mid_weight.mat │ │ │ ├── RECEPTOR snr 1 density high_weight.mat │ │ │ ├── RECEPTOR snr 1 density low_weight.mat │ │ │ ├── RECEPTOR snr 1 density mid_weight.mat │ │ │ ├── RECEPTOR snr 2 density high_weight.mat │ │ │ ├── RECEPTOR snr 2 density low_weight.mat │ │ │ ├── RECEPTOR snr 2 density mid_weight.mat │ │ │ ├── RECEPTOR snr 4 density high_weight.mat │ │ │ ├── RECEPTOR snr 4 density low_weight.mat │ │ │ ├── RECEPTOR snr 4 density mid_weight.mat │ │ │ ├── RECEPTOR snr 7 density high_weight.mat │ │ │ ├── RECEPTOR snr 7 density low_weight.mat │ │ │ ├── RECEPTOR snr 7 density mid_weight.mat │ │ │ ├── VESICLE snr 1 density high_weight.mat │ │ │ ├── VESICLE snr 1 density low_weight.mat │ │ │ ├── VESICLE snr 1 density mid_weight.mat │ │ │ ├── VESICLE snr 2 density high_weight.mat │ │ │ ├── VESICLE snr 2 density low_weight.mat │ │ │ ├── VESICLE snr 2 density mid_weight.mat │ │ │ ├── VESICLE snr 4 density high_weight.mat │ │ │ ├── VESICLE snr 4 density low_weight.mat │ │ │ ├── VESICLE snr 4 density mid_weight.mat │ │ │ ├── VESICLE snr 7 density high_weight.mat │ │ │ ├── VESICLE snr 7 density low_weight.mat │ │ │ ├── VESICLE snr 7 density mid_weight.mat │ │ │ ├── VIRUS snr 1 density high_weight.mat │ │ │ ├── VIRUS snr 1 density low_weight.mat │ │ │ ├── VIRUS snr 1 density mid_weight.mat │ │ │ ├── VIRUS snr 2 density high_weight.mat │ │ │ ├── VIRUS snr 2 density low_weight.mat │ │ │ ├── VIRUS snr 2 density mid_weight.mat │ │ │ ├── VIRUS snr 4 density high_weight.mat │ │ │ ├── VIRUS snr 4 density low_weight.mat │ │ │ ├── VIRUS snr 4 density mid_weight.mat │ │ │ ├── VIRUS snr 7 density high_weight.mat │ │ │ ├── VIRUS snr 7 density low_weight.mat │ │ │ └── VIRUS snr 7 density mid_weight.mat │ │ ├── MuSC_10x_brightfield_600microwell.mat │ │ ├── MuSC_10x_brightfield_600microwell.txt │ │ ├── NM_HSC.mat │ │ ├── NM_HSC_161119_new_template.mat │ │ ├── NM_MuSC.mat │ │ ├── NM_MuSC_all.mat │ │ ├── NM_MuSC_bgsubatten_5.mat │ │ ├── NM_MuSC_minsize_250.mat │ │ ├── NM_MuSC_prop.mat │ │ ├── TMI2015 │ │ │ ├── 130916_bgatten_5MnrPca.mat │ │ │ └── 131029_myoblasts_watershedsMnrPca.mat │ │ ├── myoblasts_10x_brightfield.mat │ │ └── myoblasts_10x_brightfield.txt │ ├── Death │ │ ├── MuSC_10x_brightfield_600microwell.mat │ │ ├── MuSC_10x_brightfield_600microwell.txt │ │ └── TMI2015 │ │ │ └── 130916_bgatten_5MnrPcaProp.mat │ ├── MotionModels │ │ ├── VIRUS snr 1 density high.mat │ │ ├── VIRUS snr 1 density low.mat │ │ ├── VIRUS snr 1 density mid.mat │ │ ├── VIRUS snr 2 density high.mat │ │ ├── VIRUS snr 2 density low.mat │ │ ├── VIRUS snr 2 density mid.mat │ │ ├── VIRUS snr 4 density high.mat │ │ ├── VIRUS snr 4 density low.mat │ │ ├── VIRUS snr 4 density mid.mat │ │ ├── VIRUS snr 7 density high.mat │ │ ├── VIRUS snr 7 density low.mat │ │ └── VIRUS snr 7 density mid.mat │ └── Split │ │ ├── MuSC_10x_brightfield_600microwell.mat │ │ ├── MuSC_10x_brightfield_600microwell.txt │ │ ├── NM_HSC.mat │ │ ├── NM_HSC_161119_new_template.mat │ │ ├── NM_MuSC.mat │ │ ├── NM_MuSC_all.mat │ │ ├── NM_MuSC_bgsubatten_5.mat │ │ ├── NM_MuSC_minsize_250.mat │ │ ├── TMI2015 │ │ ├── 130916_bgatten_5MnrPcaProp.mat │ │ └── 131029_myoblasts_watershedsMnrPcaProp.mat │ │ ├── myoblasts_10x_brightfield.mat │ │ └── myoblasts_10x_brightfield.txt ├── Deployment │ ├── BA.png │ ├── logo.png │ ├── splash.png │ ├── splash_background.png │ └── splash_background.psd ├── FindFile.m ├── Icons │ ├── FPButton.png │ ├── FPButtonPressed.png │ ├── addButton.png │ ├── addButtonPressed.png │ ├── addChildrenButton.png │ ├── addChildrenButtonPressed.png │ ├── cellEventsButton.png │ ├── cellEventsButtonPressed.png │ ├── childSplitButton.png │ ├── childSplitButtonPressed.png │ ├── colorAllButton.png │ ├── colorAllButton2.png │ ├── colorAllButton3.png │ ├── colorAllButtonPressed.png │ ├── colorButton.png │ ├── colorButtonPressed.png │ ├── coloringToolsOff.png │ ├── coloringToolsOn.png │ ├── connectButton.png │ ├── connectButtonPressed.png │ ├── continuousAddButton.png │ ├── continuousAddButtonPressed.png │ ├── correctionToolsOff.png │ ├── correctionToolsOn.png │ ├── ctcButton.png │ ├── ctcButtonPressed.png │ ├── currentLine.png │ ├── currentLinePressed.png │ ├── deleteButton.png │ ├── deleteButtonPressed.png │ ├── disappearButton.png │ ├── disappearButtonPressed.png │ ├── displayTogglesOff.png │ ├── displayTogglesOn.png │ ├── editSegmentsButton.png │ ├── editSegmentsButtonPressed.png │ ├── jump.png │ ├── microwellButton.png │ ├── microwellButtonPressed.png │ ├── moveButton.png │ ├── moveButtonPressed.png │ ├── moveMitosisButton.png │ ├── moveMitosisButtonPressed.png │ ├── negativeButton.png │ ├── negativeButtonPressed.png │ ├── outlineButton.png │ ├── outlineButtonPressed.png │ ├── plusMinusButton.png │ ├── plusMinusButtonPressed.png │ ├── positiveButton.png │ ├── positiveButtonPressed.png │ ├── removeFP.png │ ├── save.png │ ├── selectButton.png │ ├── selectButtonPressed.png │ ├── splitButton.png │ ├── splitButtonPressed.png │ ├── trackSplitButton.png │ ├── trackSplitButtonPressed.png │ ├── trajectoryButton.png │ ├── trajectoryButtonPressed.png │ ├── visualizationOff.png │ ├── visualizationOn.png │ ├── zoomButton.png │ └── zoomButtonPressed.png ├── LegacyClassifiers │ ├── Count │ │ ├── 130916_bgatten_05_selectedMnrPca.mat │ │ ├── 130916_bgatten_5_noBgMnrPca.mat │ │ ├── 130918_bgatten_5_nolightcorrectMnrPca.mat │ │ ├── 130923_bgatten_5_multlightcorrectMnrPca.mat │ │ ├── 131028_myoblasts_noBgMnrPca.mat │ │ ├── 131029_bgatten_5_noBgNoCMnrPca.mat │ │ ├── C2DL-MSC_gda.mat │ │ ├── C2DL-MSC_lda.mat │ │ ├── C2DL-MSC_mnr.mat │ │ ├── C2DL-MSC_mnr_pca.mat │ │ ├── COUNT_G__exported_Timelapse_converted_cut.mat │ │ ├── CTC_2014_LogArea_Mnr_Prop_MDA231.mat │ │ ├── Fluo-N3DL-DRO_01_cropped_weight.mat │ │ ├── HSC_130417_bootstrap.mat │ │ ├── Jeevan_120830.mat │ │ ├── Jeevan_20120830_prop.mat │ │ ├── MSC-01_MnrPca.mat │ │ ├── MSC-02_MnrPca.mat │ │ ├── MuSC_10x_20min_600mu_localvar_89feat.mat │ │ ├── MuSC_10x_20min_600mu_localvar_89feat_prop.mat │ │ ├── MuSC_10x_600mu_localvar_18feat.mat │ │ ├── MuSC_10x_600mu_localvar_81feat.mat │ │ ├── MuSC_10x_600mu_localvar_89feat.mat │ │ ├── MuSC_10x_600mu_localvar_89feat_prop.mat │ │ ├── MuSC_10x_600mu_reggrow_18feat.mat │ │ ├── MuSC_120926.mat │ │ ├── MuSC_brightfield_10x_5mon_06292012.mat │ │ ├── N2D-SIM_gda.mat │ │ ├── N2D-SIM_lda.mat │ │ ├── N2D-SIM_mnr.mat │ │ ├── N2D-SIM_mnr_pca.mat │ │ ├── N2DH-GOWT1_gda.mat │ │ ├── N2DH-GOWT1_lda.mat │ │ ├── N2DH-GOWT1_mnr.mat │ │ ├── N2DH-GOWT1_mnr_pca.mat │ │ ├── N2DL-HeLa_gda.mat │ │ ├── N2DL-HeLa_lda.mat │ │ ├── N2DL-HeLa_mnr.mat │ │ ├── N2DL-HeLa_mnr_pca.mat │ │ ├── PSC.mat │ │ ├── PSC_CTC.mat │ │ ├── PSC_equal.mat │ │ ├── Theriault_MSC-02_MnrPca.mat │ │ ├── downsample.mat │ │ ├── downsampled2.mat │ │ ├── hsc.mat │ │ ├── theriaultAlmostExtendedMnrPca.mat │ │ └── theriaultExtendedMnrPca.mat │ ├── Death │ │ ├── 130916_bgatten_05_selectedMnrPcaProp.mat │ │ ├── 130916_bgatten_5_noBgMnrPcaProp.mat │ │ ├── 130918_bgatten_5_nolightcorrectMnrPcaProp.mat │ │ ├── 130923_bgatten_5_multlightcorrectMnrPcaProp.mat │ │ ├── DEATH_G__exported_Timelapse_converted_cut.mat │ │ ├── MuSC_10x_20min_600mu_localvar_89feat_prop.mat │ │ ├── MuSC_10x_600mu_localvar_18feat.mat │ │ ├── MuSC_10x_600mu_localvar_81feat_prop.mat │ │ ├── MuSC_10x_600mu_localvar_89feat.mat │ │ ├── MuSC_10x_600mu_localvar_89feat_prop.mat │ │ ├── MuSC_10x_600mu_reggrow_18feat.mat │ │ ├── MuSC_120926.mat │ │ ├── gda_all_pair_new.mat │ │ ├── gda_forwardsearch_003.mat │ │ ├── gda_forwardsearch_010.mat │ │ ├── mnr_all_pair_new.mat │ │ ├── theriaultAlmostExtendedMnrPcaProp.mat │ │ └── theriaultExtendedMnrPcaProp.mat │ ├── Migration │ │ ├── gda_dxdy_gm_IC.mat │ │ ├── gda_forwardsearch_002.mat │ │ └── mig_gda.mat │ └── Split │ │ ├── 130916_bgatten_05_selectedMnrPcaProp.mat │ │ ├── 130916_bgatten_5_noBgMnrPcaProp.mat │ │ ├── 130918_bgatten_5_nolightcorrectMnrPcaProp.mat │ │ ├── 130923_bgatten_5_multlightcorrectMnrPcaProp.mat │ │ ├── 131028_myoblasts_noBgMnrPcaProp.mat │ │ ├── 131029_bgatten_5_noBgNoCMnrPcaProp.mat │ │ ├── C2DL-MSC_gda.mat │ │ ├── C2DL-MSC_lda.mat │ │ ├── C2DL-MSC_mnr.mat │ │ ├── C2DL-MSC_mnr_pca.mat │ │ ├── CTC_2014_Distances_2DSIM+_01.mat │ │ ├── CTC_2014_Distances_2DSIM+_02.mat │ │ ├── CTC_2014_Distances_2DSIM_01.mat │ │ ├── CTC_2014_Distances_2DSIM_02.mat │ │ ├── CTC_2014_Distances_2DSIM_03.mat │ │ ├── CTC_2014_Distances_2DSIM_04.mat │ │ ├── CTC_2014_Distances_2DSIM_05.mat │ │ ├── CTC_2014_Distances_2DSIM_06.mat │ │ ├── CTC_2014_Distances_3DSIM+_01.mat │ │ ├── CTC_2014_Distances_3DSIM+_02.mat │ │ ├── CTC_2014_Distances_3DSIM_01.mat │ │ ├── CTC_2014_Distances_3DSIM_02.mat │ │ ├── CTC_2014_Distances_3DSIM_03.mat │ │ ├── CTC_2014_Distances_3DSIM_04.mat │ │ ├── CTC_2014_Distances_3DSIM_05.mat │ │ ├── CTC_2014_Distances_3DSIM_06.mat │ │ ├── CTC_2014_Distances_HeLa_notProp.mat │ │ ├── HSC_130417_bootstrap.mat │ │ ├── MuSC_10x_20min_600mu_localvar_89feat_prop.mat │ │ ├── MuSC_10x_600mu_localvar_18feat.mat │ │ ├── MuSC_10x_600mu_localvar_81feat_prop.mat │ │ ├── MuSC_10x_600mu_localvar_89feat.mat │ │ ├── MuSC_10x_600mu_localvar_89feat_prop.mat │ │ ├── MuSC_10x_600mu_reggrow_18feat.mat │ │ ├── MuSC_120926.mat │ │ ├── N2D-SIM_gda.mat │ │ ├── N2D-SIM_lda.mat │ │ ├── N2D-SIM_mnr.mat │ │ ├── N2D-SIM_mnr_pca.mat │ │ ├── N2DH-GOWT1_gda.mat │ │ ├── N2DH-GOWT1_lda.mat │ │ ├── N2DH-GOWT1_mnr.mat │ │ ├── N2DH-GOWT1_mnr_pca.mat │ │ ├── N2DL-HeLa_gda.mat │ │ ├── N2DL-HeLa_lda.mat │ │ ├── N2DL-HeLa_mnr.mat │ │ ├── N2DL-HeLa_mnr_pca.mat │ │ ├── PSC.mat │ │ ├── SPLIT_G__exported_Timelapse_converted_cut.mat │ │ ├── downsample.mat │ │ ├── gda_all_pair_new.mat │ │ ├── gda_all_pair_new_prior.mat │ │ ├── gda_forwardsearch_003.mat │ │ ├── gda_forwardsearch_010.mat │ │ ├── mnr_all_pair_new.mat │ │ ├── theriaultAlmostExtendedMnrPcaProp.mat │ │ └── theriaultExtendedMnrPcaProp.mat ├── PSFs │ ├── BRIGHTFIELD.mat │ ├── MICROTUBULE_symmetric.mat │ ├── PSF.mat │ ├── PSF21x21_2.mat │ ├── PSF41x41.mat │ ├── RECEPTOR_symmetric.mat │ ├── VESICLE_symmetric.mat │ ├── VIRUS_2D.mat │ ├── VIRUS_symmetric.mat │ └── VIRUS_symmetric_small.mat ├── Settings │ ├── CTC2013 │ │ ├── Settings_ISBI_2013_Challenge_C2DL-MSC-01.csv │ │ ├── Settings_ISBI_2013_Challenge_C2DL-MSC-02.csv │ │ ├── Settings_ISBI_2013_Challenge_C3DH-H157-01.csv │ │ ├── Settings_ISBI_2013_Challenge_C3DH-H157-02.csv │ │ ├── Settings_ISBI_2013_Challenge_C3DL-MDA231-01.csv │ │ ├── Settings_ISBI_2013_Challenge_C3DL-MDA231-02.csv │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-01.csv │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-02.csv │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-03.csv │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-04.csv │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-05.csv │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-06.csv │ │ ├── Settings_ISBI_2013_Challenge_N2DH-GOWT1-01.csv │ │ ├── Settings_ISBI_2013_Challenge_N2DH-GOWT1-02.csv │ │ ├── Settings_ISBI_2013_Challenge_N2DL-HeLa-01.csv │ │ ├── Settings_ISBI_2013_Challenge_N2DL-HeLa-02.csv │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-01.csv │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-02.csv │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-03.csv │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-04.csv │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-05.csv │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-06.csv │ │ ├── Settings_ISBI_2013_Challenge_N3DH-CHO-01.csv │ │ ├── Settings_ISBI_2013_Challenge_N3DH-CHO-02.csv │ │ ├── Settings_ISBI_2013_Training_C2DL-MSC-01.csv │ │ ├── Settings_ISBI_2013_Training_C2DL-MSC-02.csv │ │ ├── Settings_ISBI_2013_Training_C3DH-H157-01.csv │ │ ├── Settings_ISBI_2013_Training_C3DH-H157-02.csv │ │ ├── Settings_ISBI_2013_Training_C3DL-MDA231-01.csv │ │ ├── Settings_ISBI_2013_Training_C3DL-MDA231-02.csv │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-01.csv │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-02.csv │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-03.csv │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-04.csv │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-05.csv │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-06.csv │ │ ├── Settings_ISBI_2013_Training_N2DH-GOWT1-01.csv │ │ ├── Settings_ISBI_2013_Training_N2DH-GOWT1-02.csv │ │ ├── Settings_ISBI_2013_Training_N2DL-HeLa-01.csv │ │ ├── Settings_ISBI_2013_Training_N2DL-HeLa-02.csv │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-01.csv │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-02.csv │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-03.csv │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-04.csv │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-05.csv │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-06.csv │ │ ├── Settings_ISBI_2013_Training_N3DH-CHO-01.csv │ │ └── Settings_ISBI_2013_Training_N3DH-CHO-02.csv │ ├── CTC2014 │ │ ├── Settings_ISBI_2014_Challenge_DIC-C2DH-HeLa-01.csv │ │ ├── Settings_ISBI_2014_Challenge_DIC-C2DH-HeLa-02.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C2DL-MSC-01.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C2DL-MSC-02.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C3DH-H157-01.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C3DH-H157-02.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C3DL-MDA231-01.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C3DL-MDA231-02.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-GOWT1-01.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-GOWT1-02.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM+-01.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM+-02.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-01.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-02.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-03.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-04.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-05.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-06.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DL-HeLa-01.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DL-HeLa-02.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-CE-01.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-CE-02.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-CHO-01.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-CHO-02.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM+-01.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM+-02.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-01.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-02.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-03.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-04.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-05.csv │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-06.csv │ │ ├── Settings_ISBI_2014_Challenge_PhC-C2DH-U373-01.csv │ │ ├── Settings_ISBI_2014_Challenge_PhC-C2DH-U373-02.csv │ │ ├── Settings_ISBI_2014_Challenge_PhC-C2DL-PSC-01.csv │ │ ├── Settings_ISBI_2014_Challenge_PhC-C2DL-PSC-02.csv │ │ ├── Settings_ISBI_2014_Training_DIC-C2DH-HeLa-01.csv │ │ ├── Settings_ISBI_2014_Training_DIC-C2DH-HeLa-02.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-C2DL-MSC-01.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-C2DL-MSC-02.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-C3DH-H157-01.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-C3DH-H157-02.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-C3DL-MDA231-01.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-C3DL-MDA231-02.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-GOWT1-01.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-GOWT1-02.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM+-01.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM+-02.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-01.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-02.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-03.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-04.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-05.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-06.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DL-HeLa-01.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DL-HeLa-02.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-CE-01.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-CE-02.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-CHO-01.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-CHO-02.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM+-01.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM+-02.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-01.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-02.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-03.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-04.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-05.csv │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-06.csv │ │ ├── Settings_ISBI_2014_Training_PhC-C2DH-U373-01.csv │ │ ├── Settings_ISBI_2014_Training_PhC-C2DH-U373-02.csv │ │ ├── Settings_ISBI_2014_Training_PhC-C2DL-PSC-01.csv │ │ └── Settings_ISBI_2014_Training_PhC-C2DL-PSC-02.csv │ ├── CTC2015 │ │ ├── Settings_ISBI_2015_Challenge_DIC-C2DH-HeLa-01.csv │ │ ├── Settings_ISBI_2015_Challenge_DIC-C2DH-HeLa-02.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C2DL-MSC-01.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C2DL-MSC-02.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C3DH-H157-01.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C3DH-H157-02.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C3DL-MDA231-01.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C3DL-MDA231-02.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-GOWT1-01.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-GOWT1-02.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM+-01.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM+-02.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-01.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-02.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-03.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-04.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-05.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-06.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DL-HeLa-01.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DL-HeLa-02.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-CE-01.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-CE-02.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-CHO-01.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-CHO-02.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM+-01.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM+-02.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-01.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-02.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-03.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-04.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-05.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-06.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DL-DRO-01.csv │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DL-DRO-02.csv │ │ ├── Settings_ISBI_2015_Challenge_PhC-C2DH-U373-01.csv │ │ ├── Settings_ISBI_2015_Challenge_PhC-C2DH-U373-02.csv │ │ ├── Settings_ISBI_2015_Challenge_PhC-C2DL-PSC-01.csv │ │ ├── Settings_ISBI_2015_Challenge_PhC-C2DL-PSC-02.csv │ │ ├── Settings_ISBI_2015_Training_DIC-C2DH-HeLa-01.csv │ │ ├── Settings_ISBI_2015_Training_DIC-C2DH-HeLa-02.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-C2DL-MSC-01.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-C2DL-MSC-02.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-C3DH-H157-01.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-C3DH-H157-02.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-C3DL-MDA231-01.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-C3DL-MDA231-02.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-GOWT1-01.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-GOWT1-02.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM+-01.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM+-02.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-01.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-02.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-03.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-04.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-05.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-06.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DL-HeLa-01.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DL-HeLa-02.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-CE-01.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-CE-02.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-CHO-01.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-CHO-02.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM+-01.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM+-02.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-01.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-02.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-03.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-04.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-05.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-06.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DL-DRO-01.csv │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DL-DRO-02.csv │ │ ├── Settings_ISBI_2015_Training_PhC-C2DH-U373-01.csv │ │ ├── Settings_ISBI_2015_Training_PhC-C2DH-U373-02.csv │ │ ├── Settings_ISBI_2015_Training_PhC-C2DL-PSC-01.csv │ │ └── Settings_ISBI_2015_Training_PhC-C2DL-PSC-02.csv │ ├── Fibers_high_background.csv │ ├── Fibers_low_background.csv │ ├── Fluorescence_microscopy.csv │ ├── Fusion_myotubes.csv │ ├── Fusion_nuclei.csv │ ├── ISBI2015 │ │ ├── MICROTUBULE snr 1 density high.csv │ │ ├── MICROTUBULE snr 1 density low.csv │ │ ├── MICROTUBULE snr 1 density mid.csv │ │ ├── MICROTUBULE snr 2 density high.csv │ │ ├── MICROTUBULE snr 2 density low.csv │ │ ├── MICROTUBULE snr 2 density mid.csv │ │ ├── MICROTUBULE snr 4 density high.csv │ │ ├── MICROTUBULE snr 4 density low.csv │ │ ├── MICROTUBULE snr 4 density mid.csv │ │ ├── MICROTUBULE snr 7 density high.csv │ │ ├── MICROTUBULE snr 7 density low.csv │ │ ├── MICROTUBULE snr 7 density mid.csv │ │ ├── RECEPTOR snr 1 density high.csv │ │ ├── RECEPTOR snr 1 density low.csv │ │ ├── RECEPTOR snr 1 density mid.csv │ │ ├── RECEPTOR snr 2 density high.csv │ │ ├── RECEPTOR snr 2 density low.csv │ │ ├── RECEPTOR snr 2 density mid.csv │ │ ├── RECEPTOR snr 4 density high.csv │ │ ├── RECEPTOR snr 4 density low.csv │ │ ├── RECEPTOR snr 4 density mid.csv │ │ ├── RECEPTOR snr 7 density high.csv │ │ ├── RECEPTOR snr 7 density low.csv │ │ ├── RECEPTOR snr 7 density mid.csv │ │ ├── VESICLE snr 1 density high.csv │ │ ├── VESICLE snr 1 density low.csv │ │ ├── VESICLE snr 1 density mid.csv │ │ ├── VESICLE snr 2 density high.csv │ │ ├── VESICLE snr 2 density low.csv │ │ ├── VESICLE snr 2 density mid.csv │ │ ├── VESICLE snr 4 density high.csv │ │ ├── VESICLE snr 4 density low.csv │ │ ├── VESICLE snr 4 density mid.csv │ │ ├── VESICLE snr 7 density high.csv │ │ ├── VESICLE snr 7 density low.csv │ │ ├── VESICLE snr 7 density mid.csv │ │ ├── VIRUS snr 1 density high.csv │ │ ├── VIRUS snr 1 density low.csv │ │ ├── VIRUS snr 1 density mid.csv │ │ ├── VIRUS snr 2 density high.csv │ │ ├── VIRUS snr 2 density low.csv │ │ ├── VIRUS snr 2 density mid.csv │ │ ├── VIRUS snr 4 density high.csv │ │ ├── VIRUS snr 4 density low.csv │ │ ├── VIRUS snr 4 density mid.csv │ │ ├── VIRUS snr 7 density high.csv │ │ ├── VIRUS snr 7 density low.csv │ │ └── VIRUS snr 7 density mid.csv │ ├── MuSC_10x_brightfield_600microwell.csv │ ├── Thesis2016 │ │ ├── Challenge_BF-C2DL-HSC_01.csv │ │ ├── Challenge_BF-C2DL-HSC_02.csv │ │ ├── Challenge_BF-C2DL-MRC5_01.csv │ │ ├── Challenge_BF-C2DL-MRC5_02.csv │ │ ├── Challenge_BF-C2DL-MuSC_01.csv │ │ ├── Challenge_BF-C2DL-MuSC_02.csv │ │ ├── Challenge_DIC-C2DL-MRC5_01.csv │ │ ├── Challenge_DIC-C2DL-MRC5_02.csv │ │ ├── Challenge_Fluo-C2DL-MRC5_01.csv │ │ ├── Challenge_Fluo-C2DL-MRC5_02.csv │ │ ├── Challenge_Fluo-N2DL-MRC5_01.csv │ │ ├── Challenge_Fluo-N2DL-MRC5_02.csv │ │ ├── Challenge_PhC-C2DL-MRC5_01.csv │ │ ├── Challenge_PhC-C2DL-MRC5_02.csv │ │ ├── Training_BF-C2DL-HSC_01.csv │ │ ├── Training_BF-C2DL-HSC_02.csv │ │ ├── Training_BF-C2DL-MRC5_01.csv │ │ ├── Training_BF-C2DL-MRC5_02.csv │ │ ├── Training_BF-C2DL-MuSC_01.csv │ │ ├── Training_BF-C2DL-MuSC_02.csv │ │ ├── Training_DIC-C2DL-MRC5_01.csv │ │ ├── Training_DIC-C2DL-MRC5_02.csv │ │ ├── Training_Fluo-C2DL-MRC5_01.csv │ │ ├── Training_Fluo-C2DL-MRC5_02.csv │ │ ├── Training_Fluo-N2DL-MRC5_01.csv │ │ ├── Training_Fluo-N2DL-MRC5_02.csv │ │ ├── Training_PhC-C2DL-MRC5_01.csv │ │ └── Training_PhC-C2DL-MRC5_02.csv │ ├── Transmission_microscopy.csv │ └── myoblasts_10x_brightfield.csv ├── SettingsImages │ ├── CTC2013 │ │ ├── Settings_ISBI_2013_Challenge_C2DL-MSC-01.txt │ │ ├── Settings_ISBI_2013_Challenge_C2DL-MSC-02.txt │ │ ├── Settings_ISBI_2013_Challenge_C3DH-H157-01.txt │ │ ├── Settings_ISBI_2013_Challenge_C3DH-H157-02.txt │ │ ├── Settings_ISBI_2013_Challenge_C3DL-MDA231-01.txt │ │ ├── Settings_ISBI_2013_Challenge_C3DL-MDA231-02.txt │ │ ├── Settings_ISBI_2013_Challenge_DIC-C2DH-HeLa-01.txt │ │ ├── Settings_ISBI_2013_Challenge_DIC-C2DH-HeLa-02.txt │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM+-01.txt │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM+-02.txt │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-01.txt │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-02.txt │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-03.txt │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-04.txt │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-05.txt │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-06.txt │ │ ├── Settings_ISBI_2013_Challenge_N2DH-GOWT1-01.txt │ │ ├── Settings_ISBI_2013_Challenge_N2DH-GOWT1-02.txt │ │ ├── Settings_ISBI_2013_Challenge_N2DL-HeLa-01.txt │ │ ├── Settings_ISBI_2013_Challenge_N2DL-HeLa-02.txt │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM+-01.txt │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM+-02.txt │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-01.txt │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-02.txt │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-03.txt │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-04.txt │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-05.txt │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-06.txt │ │ ├── Settings_ISBI_2013_Challenge_N3DH-CE-01.txt │ │ ├── Settings_ISBI_2013_Challenge_N3DH-CE-02.txt │ │ ├── Settings_ISBI_2013_Challenge_N3DH-CHO-01.txt │ │ ├── Settings_ISBI_2013_Challenge_N3DH-CHO-02.txt │ │ ├── Settings_ISBI_2013_Challenge_N3DL-DRO-01.txt │ │ ├── Settings_ISBI_2013_Challenge_N3DL-DRO-02.txt │ │ ├── Settings_ISBI_2013_Challenge_PhC-C2DH-U373-01.txt │ │ ├── Settings_ISBI_2013_Challenge_PhC-C2DH-U373-02.txt │ │ ├── Settings_ISBI_2013_Challenge_PhC-C2DL-PSC-01.txt │ │ ├── Settings_ISBI_2013_Challenge_PhC-C2DL-PSC-02.txt │ │ ├── Settings_ISBI_2013_Training_C2DL-MSC-01.txt │ │ ├── Settings_ISBI_2013_Training_C2DL-MSC-02.txt │ │ ├── Settings_ISBI_2013_Training_C3DH-H157-01.txt │ │ ├── Settings_ISBI_2013_Training_C3DH-H157-02.txt │ │ ├── Settings_ISBI_2013_Training_C3DL-MDA231-01.txt │ │ ├── Settings_ISBI_2013_Training_C3DL-MDA231-02.txt │ │ ├── Settings_ISBI_2013_Training_DIC-C2DH-HeLa-01.txt │ │ ├── Settings_ISBI_2013_Training_DIC-C2DH-HeLa-02.txt │ │ ├── Settings_ISBI_2013_Training_N2D-SIM+-01.txt │ │ ├── Settings_ISBI_2013_Training_N2D-SIM+-02.txt │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-01.txt │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-02.txt │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-03.txt │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-04.txt │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-05.txt │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-06.txt │ │ ├── Settings_ISBI_2013_Training_N2DH-GOWT1-01.txt │ │ ├── Settings_ISBI_2013_Training_N2DH-GOWT1-02.txt │ │ ├── Settings_ISBI_2013_Training_N2DL-HeLa-01.txt │ │ ├── Settings_ISBI_2013_Training_N2DL-HeLa-02.txt │ │ ├── Settings_ISBI_2013_Training_N3D-SIM+-01.txt │ │ ├── Settings_ISBI_2013_Training_N3D-SIM+-02.txt │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-01.txt │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-02.txt │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-03.txt │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-04.txt │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-05.txt │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-06.txt │ │ ├── Settings_ISBI_2013_Training_N3DH-CE-01.txt │ │ ├── Settings_ISBI_2013_Training_N3DH-CE-02.txt │ │ ├── Settings_ISBI_2013_Training_N3DH-CHO-01.txt │ │ ├── Settings_ISBI_2013_Training_N3DH-CHO-02.txt │ │ ├── Settings_ISBI_2013_Training_N3DL-DRO-01.txt │ │ ├── Settings_ISBI_2013_Training_N3DL-DRO-02.txt │ │ ├── Settings_ISBI_2013_Training_PhC-C2DH-U373-01.txt │ │ ├── Settings_ISBI_2013_Training_PhC-C2DH-U373-02.txt │ │ ├── Settings_ISBI_2013_Training_PhC-C2DL-PSC-01.txt │ │ └── Settings_ISBI_2013_Training_PhC-C2DL-PSC-02.txt │ ├── CTC2014 │ │ ├── Settings_ISBI_2014_Challenge_DIC-C2DH-HeLa-01.txt │ │ ├── Settings_ISBI_2014_Challenge_DIC-C2DH-HeLa-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C2DL-MSC-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C2DL-MSC-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C3DH-H157-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C3DH-H157-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C3DL-MDA231-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C3DL-MDA231-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-GOWT1-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-GOWT1-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM+-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM+-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-03.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-04.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-05.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-06.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DL-HeLa-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DL-HeLa-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-CE-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-CE-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-CHO-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-CHO-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM+-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM+-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-03.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-04.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-05.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-06.txt │ │ ├── Settings_ISBI_2014_Challenge_PhC-C2DH-U373-01.txt │ │ ├── Settings_ISBI_2014_Challenge_PhC-C2DH-U373-02.txt │ │ ├── Settings_ISBI_2014_Challenge_PhC-C2DL-PSC-01.txt │ │ ├── Settings_ISBI_2014_Challenge_PhC-C2DL-PSC-02.txt │ │ ├── Settings_ISBI_2014_Training_DIC-C2DH-HeLa-01.txt │ │ ├── Settings_ISBI_2014_Training_DIC-C2DH-HeLa-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-C2DL-MSC-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-C2DL-MSC-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-C3DH-H157-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-C3DH-H157-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-C3DL-MDA231-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-C3DL-MDA231-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-GOWT1-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-GOWT1-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM+-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM+-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-03.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-04.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-05.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-06.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DL-HeLa-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DL-HeLa-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-CE-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-CE-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-CHO-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-CHO-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM+-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM+-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-03.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-04.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-05.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-06.txt │ │ ├── Settings_ISBI_2014_Training_PhC-C2DH-U373-01.txt │ │ ├── Settings_ISBI_2014_Training_PhC-C2DH-U373-02.txt │ │ ├── Settings_ISBI_2014_Training_PhC-C2DL-PSC-01.txt │ │ └── Settings_ISBI_2014_Training_PhC-C2DL-PSC-02.txt │ ├── CTC2015 │ │ ├── Settings_ISBI_2015_Challenge_DIC-C2DH-HeLa-01.jpg │ │ ├── Settings_ISBI_2015_Challenge_DIC-C2DH-HeLa-02.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C2DL-MSC-01.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C2DL-MSC-02.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C3DH-H157-01.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C3DH-H157-02.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C3DL-MDA231-01.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C3DL-MDA231-02.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-GOWT1-01.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-GOWT1-02.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM+-01.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM+-02.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-01.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-02.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-03.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-04.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-05.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-06.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DL-HeLa-01.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DL-HeLa-02.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-CE-01.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-CE-02.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-CHO-01.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-CHO-02.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM+-01.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM+-02.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-01.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-02.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-03.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-04.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-05.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-06.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DL-DRO-01.jpg │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DL-DRO-02.jpg │ │ ├── Settings_ISBI_2015_Challenge_PhC-C2DH-U373-01.jpg │ │ ├── Settings_ISBI_2015_Challenge_PhC-C2DH-U373-02.jpg │ │ ├── Settings_ISBI_2015_Challenge_PhC-C2DL-PSC-01.jpg │ │ ├── Settings_ISBI_2015_Challenge_PhC-C2DL-PSC-02.jpg │ │ ├── Settings_ISBI_2015_Training_DIC-C2DH-HeLa-01.jpg │ │ ├── Settings_ISBI_2015_Training_DIC-C2DH-HeLa-02.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-C2DL-MSC-01.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-C2DL-MSC-02.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-C3DH-H157-01.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-C3DH-H157-02.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-C3DL-MDA231-01.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-C3DL-MDA231-02.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-GOWT1-01.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-GOWT1-02.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM+-01.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM+-02.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-01.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-02.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-03.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-04.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-05.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-06.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DL-HeLa-01.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DL-HeLa-02.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-CE-01.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-CE-02.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-CHO-01.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-CHO-02.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM+-01.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM+-02.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-01.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-02.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-03.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-04.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-05.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-06.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DL-DRO-01.jpg │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DL-DRO-02.jpg │ │ ├── Settings_ISBI_2015_Training_PhC-C2DH-U373-01.jpg │ │ ├── Settings_ISBI_2015_Training_PhC-C2DH-U373-02.jpg │ │ ├── Settings_ISBI_2015_Training_PhC-C2DL-PSC-01.jpg │ │ └── Settings_ISBI_2015_Training_PhC-C2DL-PSC-02.jpg │ ├── Fibers_high_background.jpg │ ├── Fibers_low_background.jpg │ ├── Fluorescence_microscopy.txt │ ├── Fusion_myotubes.jpg │ ├── Fusion_nuclei.jpg │ ├── ISBI2015 │ │ ├── MICROTUBULE snr 1 density high.jpg │ │ ├── MICROTUBULE snr 1 density low.jpg │ │ ├── MICROTUBULE snr 1 density mid.jpg │ │ ├── MICROTUBULE snr 2 density high.jpg │ │ ├── MICROTUBULE snr 2 density low.jpg │ │ ├── MICROTUBULE snr 2 density mid.jpg │ │ ├── MICROTUBULE snr 4 density high.jpg │ │ ├── MICROTUBULE snr 4 density low.jpg │ │ ├── MICROTUBULE snr 4 density mid.jpg │ │ ├── MICROTUBULE snr 7 density high.jpg │ │ ├── MICROTUBULE snr 7 density low.jpg │ │ ├── MICROTUBULE snr 7 density mid.jpg │ │ ├── RECEPTOR snr 1 density high.jpg │ │ ├── RECEPTOR snr 1 density low.jpg │ │ ├── RECEPTOR snr 1 density mid.jpg │ │ ├── RECEPTOR snr 2 density high.jpg │ │ ├── RECEPTOR snr 2 density low.jpg │ │ ├── RECEPTOR snr 2 density mid.jpg │ │ ├── RECEPTOR snr 4 density high.jpg │ │ ├── RECEPTOR snr 4 density low.jpg │ │ ├── RECEPTOR snr 4 density mid.jpg │ │ ├── RECEPTOR snr 7 density high.jpg │ │ ├── RECEPTOR snr 7 density low.jpg │ │ ├── RECEPTOR snr 7 density mid.jpg │ │ ├── VESICLE snr 1 density high.jpg │ │ ├── VESICLE snr 1 density low.jpg │ │ ├── VESICLE snr 1 density mid.jpg │ │ ├── VESICLE snr 2 density high.jpg │ │ ├── VESICLE snr 2 density low.jpg │ │ ├── VESICLE snr 2 density mid.jpg │ │ ├── VESICLE snr 4 density high.jpg │ │ ├── VESICLE snr 4 density low.jpg │ │ ├── VESICLE snr 4 density mid.jpg │ │ ├── VESICLE snr 7 density high.jpg │ │ ├── VESICLE snr 7 density low.jpg │ │ ├── VESICLE snr 7 density mid.jpg │ │ ├── VIRUS snr 1 density high.jpg │ │ ├── VIRUS snr 1 density low.jpg │ │ ├── VIRUS snr 1 density mid.jpg │ │ ├── VIRUS snr 2 density high.jpg │ │ ├── VIRUS snr 2 density low.jpg │ │ ├── VIRUS snr 2 density mid.jpg │ │ ├── VIRUS snr 4 density high.jpg │ │ ├── VIRUS snr 4 density low.jpg │ │ ├── VIRUS snr 4 density mid.jpg │ │ ├── VIRUS snr 7 density high.jpg │ │ ├── VIRUS snr 7 density low.jpg │ │ └── VIRUS snr 7 density mid.jpg │ ├── MuSC_10x_brightfield_600microwell.jpg │ ├── Thesis2016 │ │ ├── Challenge_BF-C2DL-HSC_01.jpg │ │ ├── Challenge_BF-C2DL-HSC_02.jpg │ │ ├── Challenge_BF-C2DL-MRC5_01.jpg │ │ ├── Challenge_BF-C2DL-MRC5_02.jpg │ │ ├── Challenge_BF-C2DL-MuSC_01.jpg │ │ ├── Challenge_BF-C2DL-MuSC_02.jpg │ │ ├── Challenge_DIC-C2DL-MRC5_01.jpg │ │ ├── Challenge_DIC-C2DL-MRC5_02.jpg │ │ ├── Challenge_Fluo-C2DL-MRC5_01.jpg │ │ ├── Challenge_Fluo-C2DL-MRC5_02.jpg │ │ ├── Challenge_Fluo-N2DL-MRC5_01.jpg │ │ ├── Challenge_Fluo-N2DL-MRC5_02.jpg │ │ ├── Challenge_PhC-C2DL-MRC5_01.jpg │ │ ├── Challenge_PhC-C2DL-MRC5_02.jpg │ │ ├── Training_BF-C2DL-HSC_01.jpg │ │ ├── Training_BF-C2DL-HSC_02.jpg │ │ ├── Training_BF-C2DL-MRC5_01.jpg │ │ ├── Training_BF-C2DL-MRC5_02.jpg │ │ ├── Training_BF-C2DL-MuSC_01.jpg │ │ ├── Training_BF-C2DL-MuSC_02.jpg │ │ ├── Training_DIC-C2DL-MRC5_01.jpg │ │ ├── Training_DIC-C2DL-MRC5_02.jpg │ │ ├── Training_Fluo-C2DL-MRC5_01.jpg │ │ ├── Training_Fluo-C2DL-MRC5_02.jpg │ │ ├── Training_Fluo-N2DL-MRC5_01.jpg │ │ ├── Training_Fluo-N2DL-MRC5_02.jpg │ │ ├── Training_PhC-C2DL-MRC5_01.jpg │ │ └── Training_PhC-C2DL-MRC5_02.jpg │ ├── Transmission_microscopy.jpg │ └── myoblasts_10x_brightfield.jpg ├── SettingsInfo │ ├── CTC2013 │ │ ├── Settings_ISBI_2013_Challenge_C2DL-MSC-01.txt │ │ ├── Settings_ISBI_2013_Challenge_C2DL-MSC-02.txt │ │ ├── Settings_ISBI_2013_Challenge_C3DH-H157-01.txt │ │ ├── Settings_ISBI_2013_Challenge_C3DH-H157-02.txt │ │ ├── Settings_ISBI_2013_Challenge_C3DL-MDA231-01.txt │ │ ├── Settings_ISBI_2013_Challenge_C3DL-MDA231-02.txt │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-01.txt │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-02.txt │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-03.txt │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-04.txt │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-05.txt │ │ ├── Settings_ISBI_2013_Challenge_N2D-SIM-06.txt │ │ ├── Settings_ISBI_2013_Challenge_N2DH-GOWT1-01.txt │ │ ├── Settings_ISBI_2013_Challenge_N2DH-GOWT1-02.txt │ │ ├── Settings_ISBI_2013_Challenge_N2DL-HeLa-01.txt │ │ ├── Settings_ISBI_2013_Challenge_N2DL-HeLa-02.txt │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-01.txt │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-02.txt │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-03.txt │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-04.txt │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-05.txt │ │ ├── Settings_ISBI_2013_Challenge_N3D-SIM-06.txt │ │ ├── Settings_ISBI_2013_Challenge_N3DH-CHO-01.txt │ │ ├── Settings_ISBI_2013_Challenge_N3DH-CHO-02.txt │ │ ├── Settings_ISBI_2013_Training_C2DL-MSC-01.txt │ │ ├── Settings_ISBI_2013_Training_C2DL-MSC-02.txt │ │ ├── Settings_ISBI_2013_Training_C3DH-H157-01.txt │ │ ├── Settings_ISBI_2013_Training_C3DH-H157-02.txt │ │ ├── Settings_ISBI_2013_Training_C3DL-MDA231-01.txt │ │ ├── Settings_ISBI_2013_Training_C3DL-MDA231-02.txt │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-01.txt │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-02.txt │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-03.txt │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-04.txt │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-05.txt │ │ ├── Settings_ISBI_2013_Training_N2D-SIM-06.txt │ │ ├── Settings_ISBI_2013_Training_N2DH-GOWT1-01.txt │ │ ├── Settings_ISBI_2013_Training_N2DH-GOWT1-02.txt │ │ ├── Settings_ISBI_2013_Training_N2DL-HeLa-01.txt │ │ ├── Settings_ISBI_2013_Training_N2DL-HeLa-02.txt │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-01.txt │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-02.txt │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-03.txt │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-04.txt │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-05.txt │ │ ├── Settings_ISBI_2013_Training_N3D-SIM-06.txt │ │ ├── Settings_ISBI_2013_Training_N3DH-CHO-01.txt │ │ └── Settings_ISBI_2013_Training_N3DH-CHO-02.txt │ ├── CTC2014 │ │ ├── Settings_ISBI_2014_Challenge_DIC-C2DH-HeLa-01.txt │ │ ├── Settings_ISBI_2014_Challenge_DIC-C2DH-HeLa-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C2DL-MSC-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C2DL-MSC-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C3DH-H157-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C3DH-H157-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C3DL-MDA231-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-C3DL-MDA231-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-GOWT1-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-GOWT1-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM+-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM+-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-03.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-04.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-05.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DH-SIM-06.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DL-HeLa-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N2DL-HeLa-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-CE-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-CE-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-CHO-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-CHO-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM+-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM+-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-01.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-02.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-03.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-04.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-05.txt │ │ ├── Settings_ISBI_2014_Challenge_Fluo-N3DH-SIM-06.txt │ │ ├── Settings_ISBI_2014_Challenge_PhC-C2DH-U373-01.txt │ │ ├── Settings_ISBI_2014_Challenge_PhC-C2DH-U373-02.txt │ │ ├── Settings_ISBI_2014_Challenge_PhC-C2DL-PSC-01.txt │ │ ├── Settings_ISBI_2014_Challenge_PhC-C2DL-PSC-02.txt │ │ ├── Settings_ISBI_2014_Training_DIC-C2DH-HeLa-01.txt │ │ ├── Settings_ISBI_2014_Training_DIC-C2DH-HeLa-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-C2DL-MSC-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-C2DL-MSC-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-C3DH-H157-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-C3DH-H157-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-C3DL-MDA231-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-C3DL-MDA231-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-GOWT1-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-GOWT1-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM+-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM+-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-03.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-04.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-05.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DH-SIM-06.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DL-HeLa-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N2DL-HeLa-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-CE-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-CE-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-CHO-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-CHO-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM+-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM+-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-01.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-02.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-03.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-04.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-05.txt │ │ ├── Settings_ISBI_2014_Training_Fluo-N3DH-SIM-06.txt │ │ ├── Settings_ISBI_2014_Training_PhC-C2DH-U373-01.txt │ │ ├── Settings_ISBI_2014_Training_PhC-C2DH-U373-02.txt │ │ ├── Settings_ISBI_2014_Training_PhC-C2DL-PSC-01.txt │ │ └── Settings_ISBI_2014_Training_PhC-C2DL-PSC-02.txt │ ├── CTC2015 │ │ ├── Settings_ISBI_2015_Challenge_DIC-C2DH-HeLa-01.txt │ │ ├── Settings_ISBI_2015_Challenge_DIC-C2DH-HeLa-02.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C2DL-MSC-01.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C2DL-MSC-02.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C3DH-H157-01.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C3DH-H157-02.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C3DL-MDA231-01.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-C3DL-MDA231-02.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-GOWT1-01.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-GOWT1-02.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM+-01.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM+-02.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-01.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-02.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-03.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-04.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-05.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DH-SIM-06.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DL-HeLa-01.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N2DL-HeLa-02.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-CE-01.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-CE-02.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-CHO-01.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-CHO-02.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM+-01.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM+-02.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-01.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-02.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-03.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-04.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-05.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DH-SIM-06.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DL-DRO-01.txt │ │ ├── Settings_ISBI_2015_Challenge_Fluo-N3DL-DRO-02.txt │ │ ├── Settings_ISBI_2015_Challenge_PhC-C2DH-U373-01.txt │ │ ├── Settings_ISBI_2015_Challenge_PhC-C2DH-U373-02.txt │ │ ├── Settings_ISBI_2015_Challenge_PhC-C2DL-PSC-01.txt │ │ ├── Settings_ISBI_2015_Challenge_PhC-C2DL-PSC-02.txt │ │ ├── Settings_ISBI_2015_Training_DIC-C2DH-HeLa-01.txt │ │ ├── Settings_ISBI_2015_Training_DIC-C2DH-HeLa-02.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-C2DL-MSC-01.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-C2DL-MSC-02.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-C3DH-H157-01.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-C3DH-H157-02.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-C3DL-MDA231-01.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-C3DL-MDA231-02.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-GOWT1-01.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-GOWT1-02.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM+-01.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM+-02.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-01.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-02.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-03.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-04.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-05.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DH-SIM-06.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DL-HeLa-01.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N2DL-HeLa-02.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-CE-01.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-CE-02.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-CHO-01.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-CHO-02.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM+-01.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM+-02.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-01.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-02.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-03.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-04.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-05.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DH-SIM-06.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DL-DRO-01.txt │ │ ├── Settings_ISBI_2015_Training_Fluo-N3DL-DRO-02.txt │ │ ├── Settings_ISBI_2015_Training_PhC-C2DH-U373-01.txt │ │ ├── Settings_ISBI_2015_Training_PhC-C2DH-U373-02.txt │ │ ├── Settings_ISBI_2015_Training_PhC-C2DL-PSC-01.txt │ │ └── Settings_ISBI_2015_Training_PhC-C2DL-PSC-02.txt │ ├── Fibers_high_background.txt │ ├── Fibers_low_background.txt │ ├── Fluorescence_microscopy.txt │ ├── Fusion_myotubes.txt │ ├── Fusion_nuclei.txt │ ├── ISBI2015 │ │ ├── MICROTUBULE snr 1 density high.txt │ │ ├── MICROTUBULE snr 1 density low.txt │ │ ├── MICROTUBULE snr 1 density mid.txt │ │ ├── MICROTUBULE snr 2 density high.txt │ │ ├── MICROTUBULE snr 2 density low.txt │ │ ├── MICROTUBULE snr 2 density mid.txt │ │ ├── MICROTUBULE snr 4 density high.txt │ │ ├── MICROTUBULE snr 4 density low.txt │ │ ├── MICROTUBULE snr 4 density mid.txt │ │ ├── MICROTUBULE snr 7 density high.txt │ │ ├── MICROTUBULE snr 7 density low.txt │ │ ├── MICROTUBULE snr 7 density mid.txt │ │ ├── RECEPTOR snr 1 density high.txt │ │ ├── RECEPTOR snr 1 density low.txt │ │ ├── RECEPTOR snr 1 density mid.txt │ │ ├── RECEPTOR snr 2 density high.txt │ │ ├── RECEPTOR snr 2 density low.txt │ │ ├── RECEPTOR snr 2 density mid.txt │ │ ├── RECEPTOR snr 4 density high.txt │ │ ├── RECEPTOR snr 4 density low.txt │ │ ├── RECEPTOR snr 4 density mid.txt │ │ ├── RECEPTOR snr 7 density high.txt │ │ ├── RECEPTOR snr 7 density low.txt │ │ ├── RECEPTOR snr 7 density mid.txt │ │ ├── VESICLE snr 1 density high.txt │ │ ├── VESICLE snr 1 density low.txt │ │ ├── VESICLE snr 1 density mid.txt │ │ ├── VESICLE snr 2 density high.txt │ │ ├── VESICLE snr 2 density low.txt │ │ ├── VESICLE snr 2 density mid.txt │ │ ├── VESICLE snr 4 density high.txt │ │ ├── VESICLE snr 4 density low.txt │ │ ├── VESICLE snr 4 density mid.txt │ │ ├── VESICLE snr 7 density high.txt │ │ ├── VESICLE snr 7 density low.txt │ │ ├── VESICLE snr 7 density mid.txt │ │ ├── VIRUS snr 1 density high.txt │ │ ├── VIRUS snr 1 density low.txt │ │ ├── VIRUS snr 1 density mid.txt │ │ ├── VIRUS snr 2 density high.txt │ │ ├── VIRUS snr 2 density low.txt │ │ ├── VIRUS snr 2 density mid.txt │ │ ├── VIRUS snr 4 density high.txt │ │ ├── VIRUS snr 4 density low.txt │ │ ├── VIRUS snr 4 density mid.txt │ │ ├── VIRUS snr 7 density high.txt │ │ ├── VIRUS snr 7 density low.txt │ │ └── VIRUS snr 7 density mid.txt │ ├── MuSC_10x_brightfield_600microwell.txt │ ├── NM2016 │ │ ├── HSC_B01_17.txt │ │ ├── HSC_B01_24.txt │ │ ├── MRC-5_brightfield_B02_01.txt │ │ ├── MRC-5_brightfield_B02_03.txt │ │ ├── MRC-5_brightfield_B03_03.txt │ │ ├── MRC-5_brightfield_C02_03.txt │ │ ├── MRC-5_dic_B02_01.txt │ │ ├── MRC-5_dic_B02_03.txt │ │ ├── MRC-5_dic_B03_03.txt │ │ ├── MRC-5_dic_C02_03.txt │ │ ├── MRC-5_fluor_cytoplasm_B02_01.txt │ │ ├── MRC-5_fluor_cytoplasm_B02_03.txt │ │ ├── MRC-5_fluor_cytoplasm_B03_03.txt │ │ ├── MRC-5_fluor_cytoplasm_C02_03.txt │ │ ├── MRC-5_fluor_nuclear_B02_01.txt │ │ ├── MRC-5_fluor_nuclear_B02_03.txt │ │ ├── MRC-5_fluor_nuclear_B03_03.txt │ │ ├── MRC-5_fluor_nuclear_C02_03.txt │ │ ├── MRC-5_phase_B02_01.txt │ │ ├── MRC-5_phase_B02_03.txt │ │ ├── MRC-5_phase_B03_03.txt │ │ ├── MRC-5_phase_C02_03.txt │ │ ├── MuSC_B02_18.txt │ │ ├── MuSC_B04_03.txt │ │ ├── MuSC_C02_02.txt │ │ ├── MuSC_C02_05.txt │ │ ├── MuSC_C02_27.txt │ │ └── MuSC_D05_24.txt │ ├── Transmission_microscopy.txt │ └── myoblasts_10x_brightfield.txt ├── Templates │ ├── HSC_10x_bf_21x21.mat │ └── HSC_training_01_550_smaller.mat └── version.txt ├── GUIs ├── AboutBaxterAlgorithms.m ├── CTCExportGUI.m ├── CentralNucleiGUI.m ├── CuttingGUI.m ├── DataManipulation │ ├── ConcatenateExperimentsGUI.m │ ├── ConvertMergedImagesGUI.m │ ├── CopyOrMoveSequences.m │ ├── CopyOrMoveVersion.m │ ├── CopySequences.m │ ├── DeleteSequences.m │ ├── DeleteVersion.m │ ├── MoveSequences.m │ └── RemoveVersion.m ├── ExportStatistics.m ├── FiberAnalysisGUI.m ├── FusionIndexGUI.m ├── InfoDialog.m ├── LoadSettingsGUI.m ├── LoadSettingsImageGUI.m ├── Logs │ ├── EditStrToFileStr.m │ ├── FileStrToEditStr.m │ ├── ReadLogNote.m │ └── WriteLog.m ├── Menus │ ├── CreateMenus.m │ ├── GetMenu.m │ └── SetVisibleMenus.m ├── Players │ ├── CTCControlPlayer.m │ ├── CellAnalysisPlayer.m │ ├── ControlPlayer.m │ ├── ManualCorrectionPlayer.m │ ├── ManualFiberCorrectionPlayer.m │ ├── SegmentationPlayer.m │ ├── SequencePlayer.m │ ├── SetFluorescencePlayer.m │ ├── UI Controls │ │ ├── ChannelGradient.m │ │ ├── ChannelHistogram.m │ │ ├── PushButton.m │ │ └── ToggleButton.m │ ├── ZControlPlayer.m │ └── ZPlayer.m ├── PopulationAnalysisGUI.m ├── Queue.m ├── Record │ ├── PadForFFDshow.m │ ├── RecordAxes.m │ └── RecordGUI.m ├── ReplaceSegmentation.m ├── SavePlotsGUI.m ├── SaveSettingsGUI.m ├── SegmentationOptimization.m ├── SettingsGUI.m ├── StabilizationGUI.m ├── TrackingGUI.m └── TrainClassifierGUI.m ├── ImageData ├── CutPixelRegion.m ├── GetWellCircle.m ├── ImageData.m └── MergeImage.m ├── LICENSE ├── PerformanceEvalution ├── AOGMR.m ├── AOGMR_BLACK.m ├── PerformanceSEG.m ├── PerformanceSEGGUI.m ├── PerformanceTRA.m ├── PerformanceTRAGUI.m └── SEGmeasure.m ├── Preprocessing ├── BgSubtraction │ ├── Attenuate.m │ ├── BgImage_median.m │ ├── BgImage_min.m │ ├── BgSubDisplay.m │ ├── BgSub_generic.m │ ├── BgSub_median.m │ ├── BgSub_medianfit.m │ ├── BgSub_min.m │ └── MediaChange2TLims.m ├── Cut │ ├── Cut.m │ └── FindWellsHough.m └── Stabilization │ ├── CropExtrapolatedPixels.m │ ├── ReadStabilizationLog.m │ ├── StabilizeLK.m │ └── WriteStabilizationLog.m ├── README.md ├── ReleaseNotes ├── ReleaseNotes.pdf └── ReleaseNotes.tex ├── Scores ├── Appear │ ├── AppearanceScores.m │ └── AppearanceScores_PHD.m ├── Classifiers │ ├── ChangePriors.m │ ├── Classify.m │ ├── DataSet.m │ ├── FindDeaths.m │ ├── FindSplits.m │ ├── GetClassifierPath.m │ ├── NecessaryFeatures.m │ ├── ReplaceNanProbs.m │ ├── SplitDataSet.m │ ├── Train.m │ ├── TrainClassifiers.m │ └── TrainWeights.m ├── Count │ ├── CountScores.m │ └── ExtrapProbs.m ├── Death │ └── DeathScores.m ├── Disappear │ ├── DisappearanceScores.m │ └── DisappearanceScores_PHD.m ├── Features │ ├── AddCellProfilerFeatures.m │ ├── FeatureMatrix.m │ ├── Frame.m │ ├── Generic │ │ ├── ComputeFeatures.m │ │ ├── GetExtraArguments.m │ │ ├── ImageProcessor.m │ │ └── SubstituteFeatureNames.m │ ├── GenericFeatures │ │ ├── Area.m │ │ ├── CenterDistance.m │ │ ├── GradientComponent.m │ │ └── PairFeatures │ │ │ └── Jaccard.m │ ├── ISBI12Features │ │ ├── AxisRatio.m │ │ ├── Compactness.m │ │ ├── ConvCompHeightMean.m │ │ ├── ConvHeightMean.m │ │ ├── ConvHeightNorm.m │ │ ├── ConvVolMean.m │ │ ├── ConvexArea.m │ │ ├── ConvexAreaNorm.m │ │ ├── Curvature.m │ │ ├── DistTo.m │ │ ├── EdgeDistMaxNorm.m │ │ ├── EdgeDistMeanNorm.m │ │ ├── GradMagMean.m │ │ ├── Height.m │ │ ├── HeightMean.m │ │ ├── IBoundary.m │ │ ├── ICenter.m │ │ ├── ICentroid.m │ │ ├── IDistPower.m │ │ ├── IFraction.m │ │ ├── InvCompactness.m │ │ ├── MeanDistBetween.m │ │ ├── Perimeter.m │ │ ├── PerimeterNorm.m │ │ └── Smoothness.m │ ├── ISBI2012Features.m │ ├── ReplaceNanFeatures.m │ ├── SelectFeatures.m │ ├── TheriaultFeatures.m │ ├── Theriault_features │ │ ├── BoundaryCentroidDist.m │ │ ├── CentroidX.m │ │ ├── CentroidY.m │ │ ├── Circularity.m │ │ ├── Dispersion.m │ │ ├── Elongation.m │ │ ├── Extension.m │ │ ├── Hu.m │ │ ├── ShapeFactor.m │ │ └── Texture.m │ ├── TransmissionFeatures.m │ └── ZeroBorders.m ├── Migration │ ├── MigLogLikeList_3D.m │ ├── MigLogLikeList_Jaccard.m │ ├── MigLogLikeList_PHD_DRO.m │ ├── MigLogLikeList_PHD_ISBI_IMM.m │ ├── MigLogLikeList_PHD_ISBI_tracks.m │ ├── MigLogLikeList_uniformClutter.m │ ├── MigLogLikeList_viterbiPaper.m │ └── MigrationScores_generic.m ├── NClosest.m └── Split │ └── SplitScores.m ├── Segmentation ├── LocalVariance │ ├── Ellipse.m │ ├── LocalVariance.m │ ├── LocalVariance_gauss.m │ └── Segment_localvariance.m ├── Optimization │ ├── CTCSegmentation.m │ ├── CoordinateDescent.m │ ├── ErosionGrid.m │ ├── GoldenSectionSearch.m │ ├── Optimizer.m │ ├── SEGOptimizerEx.m │ └── SEGOptimizerSeq.m ├── PixelsBetween.m ├── SegmentSequence.m ├── Segment_bandpass.m ├── Segment_bandpass3D.m ├── Segment_fibers.m ├── Segment_generic.m ├── Segment_generic3D.m ├── Segment_import.m ├── Segment_import_binary.m ├── Segment_precondPSF.m ├── Segment_precondPSF3D.m ├── Segment_ridgeconnection.m ├── Segment_template.m ├── Segment_threshold.m ├── Segment_threshold3D.m ├── Smooth.m ├── SmoothComp.m ├── SubPixelMaximaWeighting.m ├── SubPixelMaximaWeighting3D.m ├── SwitchSegmentation.m └── Watershed │ ├── ArraySave.cpp │ ├── ArraySave.h │ ├── Border.cpp │ ├── Border.h │ ├── Corner.cpp │ ├── Corner.h │ ├── DownSampleZ.m │ ├── MergeSegments.cpp │ ├── MergeSegments.h │ ├── MergeWatersheds.cpp │ ├── MergeWatersheds.mexa64 │ ├── MergeWatersheds.mexmaci64 │ ├── MergeWatersheds.mexw64 │ ├── Region.cpp │ ├── Region.h │ ├── RemoveWatershedRidges.m │ ├── SeededWatershed.cpp │ ├── SeededWatershed.mexa64 │ ├── SeededWatershed.mexmaci64 │ ├── SeededWatershed.mexw64 │ ├── Segment.cpp │ ├── Segment.h │ ├── StretchZ.m │ ├── Surface.cpp │ ├── Surface.h │ ├── SurfaceComparator.cpp │ ├── SurfaceComparator.h │ ├── UpSampleZ.m │ └── WatershedLabels.m ├── Settings ├── AllSettings.m ├── CopySettings.m ├── DeleteSettings.m ├── GetSeqSettings.m ├── GetSettingsPath.m ├── ImageParameters.m ├── Map.m ├── MergeSettings.m ├── ReadDelimMat.m ├── ReadSeqSettings.m ├── ReadSettings.m ├── SetSeqSettings.m ├── Setting.m ├── SettingsPanel.m ├── WriteDelimMat.m ├── WriteSeqSettings.m └── WriteSettings.m ├── Tracking ├── ApplyOffsets.m ├── BipartiteMatch.m ├── BipartiteMatch_correction.m ├── BreakClusters.m ├── FPTrack.m ├── FalseBlobs.m ├── GMPHD │ ├── AppearanceCovBrownian.m │ ├── AppearanceCovLinear.m │ ├── CellPHD.m │ ├── CellPHD_IMM.m │ ├── ComputeGMPHD.m │ ├── ComputeGMPHD_IMM.m │ ├── GMMmergeKLdiv.m │ ├── GMSegments.m │ ├── GammaBorders.m │ ├── GaussPDF.m │ └── Parameters_GMPHD.m ├── Hungarian │ ├── Hungarian.cpp │ ├── Hungarian.mexa64 │ ├── Hungarian.mexmaci64 │ └── Hungarian.mexw64 ├── KMeansSplit.m ├── Matrix2Cell.m ├── SaveTrack.m ├── Track.m └── Viterbi │ ├── Apoptosis.cpp │ ├── Apoptosis.h │ ├── Appearance.cpp │ ├── Appearance.h │ ├── Arc.cpp │ ├── Arc.h │ ├── ArraySave.cpp │ ├── ArraySave.h │ ├── CellNode.cpp │ ├── CellNode.h │ ├── CellTrellis.cpp │ ├── CellTrellis.h │ ├── Count.cpp │ ├── Count.h │ ├── Detection.cpp │ ├── Detection.h │ ├── Disappearance.cpp │ ├── Disappearance.h │ ├── Event.cpp │ ├── Event.h │ ├── FreeArc.cpp │ ├── FreeArc.h │ ├── FreeArcNoSwap.cpp │ ├── FreeArcNoSwap.h │ ├── IdleState.cpp │ ├── IdleState.h │ ├── LogStream.cpp │ ├── LogStream.h │ ├── LogStreamBuffer.cpp │ ├── LogStreamBuffer.h │ ├── MergeBrokenBlobs.m │ ├── MergeFPWatersheds.m │ ├── MergeFPWatersheds3D.m │ ├── MergeOverlappingFP.m │ ├── Migration.cpp │ ├── Migration.h │ ├── Mitosis.cpp │ ├── Mitosis.h │ ├── Node.cpp │ ├── Node.h │ ├── Persist.cpp │ ├── Persist.h │ ├── Preexist.cpp │ ├── Preexist.h │ ├── State.cpp │ ├── State.h │ ├── Swap.cpp │ ├── Swap.h │ ├── Tree.cpp │ ├── Tree.h │ ├── Trellis.cpp │ ├── Trellis.h │ ├── Variable.cpp │ ├── Variable.h │ ├── ViterbiTrackLinking.cpp │ ├── ViterbiTrackLinking.mexa64 │ ├── ViterbiTrackLinking.mexmaci64 │ └── ViterbiTrackLinking.mexw64 ├── UserGuide ├── IEEEbib.bst ├── UserGuide.pdf ├── UserGuide.tex ├── correctionTable.tex ├── figures │ ├── 3Dplayers.png │ ├── MuSC.png │ ├── MuSC_bgsub.png │ ├── cellAnalysisGUI.png │ ├── classifierTrainingGUI.png │ ├── correctionGUI.png │ ├── countPlot.pdf │ ├── eventCountingGUI.png │ ├── fibers.png │ ├── fluorescenceGUI.png │ ├── fluorescenceMerge.png │ ├── fusionIndexGUI.png │ ├── loadSettings.png │ ├── mainGUI.png │ ├── myotubes.png │ ├── myotubes_analyzed.png │ ├── plotGUI.png │ ├── populationAnalysisGUI.png │ ├── scatterPlotGUI.png │ ├── segmentationGUI.png │ ├── segmentationOptimization.png │ ├── settingsGUI.png │ └── trackingGUI.png ├── postSegmentationTable.tex ├── refs.bib └── trackTable.tex ├── Utilities ├── ApplyToFolder.m ├── CTCGTPlanes.m ├── GetArgs.m ├── GetVersions.m ├── GreenToRed.m ├── HasVersion.m ├── InsideAxes.m ├── IsGrayRGB.m ├── JavaPaths │ ├── AddJavaPaths.m │ ├── CheckJavaPaths.m │ └── RequiredJavaPaths.m ├── LoadVariable.m ├── MakeUnique.m ├── MaxWorkers.m ├── MeanNoNan.m ├── MinSquareDist.m ├── ModIndex.m ├── PTC12parameters.m ├── Paths │ ├── FileEnd.m │ ├── FileParts2.m │ ├── FileType.m │ ├── GetNames.m │ ├── GetSeqDirs.m │ └── GetUseSeq.m ├── Restart.m ├── SaveVariable.m ├── SelectArgs.m ├── SetKeyPressCallback.m ├── SetKeyReleaseCallback.m ├── SpecChar.m 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