├── .gitignore ├── LICENSE ├── README.md ├── apt.txt ├── claire └── macro-coloc-fix │ └── CL_coloc_2.ijm ├── clement ├── macros │ ├── automate-kymo │ │ └── Analyse_kymo_live.ijm │ ├── cells-detection │ │ ├── Batch_Count_Maximas.py │ │ ├── Count_Nuclei.py │ │ ├── Points_From_Labels.py │ │ ├── README.md │ │ ├── Update_CSV.py │ │ ├── current.classifier │ │ ├── current.labeling │ │ └── make_training_serie.py │ ├── count-dapi-vs-ki67 │ │ ├── README.md │ │ └── count-cells.ijm │ ├── count-spots-per-nucleus │ │ ├── segment-nuclei.ijm │ │ └── spots-per-nucleus.ijm │ ├── death-ratio-teeth │ │ └── cover-rate.py │ ├── exclusive-co-occs │ │ ├── 01-crop-stacks.ijm │ │ ├── 02-make-proj.ijm │ │ ├── 03-cellpose2d.py │ │ ├── 03-check-cp.ijm │ │ ├── 04-make-label-stacks.ijm │ │ ├── 05-find-spots.py │ │ ├── 06-aggregate-results.py │ │ ├── README.md │ │ └── filter-slide-spots.py │ ├── find-rings │ │ ├── measure-ratios.ijm │ │ └── projection.ijm │ ├── general │ │ └── Random_LUT.py │ ├── histogram-crop │ │ └── rescale-histogram.py │ ├── int-around-nuclei │ │ └── measure-intensity.ijm │ ├── md-yeasts │ │ ├── #old# │ │ │ ├── curvature.py │ │ │ ├── makeNGone_v0.py │ │ │ └── testDistances.py │ │ ├── MD_Batch_Yeasts.py │ │ ├── MD_Export_ROI_Manager.py │ │ ├── MD_Options.py │ │ └── MD_Yeasts.py │ ├── measure-metaxylems │ │ ├── macro-metaxylems.ijm │ │ └── macro-stele.ijm │ ├── misc │ │ ├── install-mdyeasts.py │ │ └── install-nucleitools.py │ ├── mitotic-spindle-segmentation │ │ ├── script-fuseaux-evo.py │ │ └── script-fuseaux.py │ ├── multiple-co-occurences │ │ ├── README.md │ │ ├── count-nuclei.py │ │ ├── crop-folder.ijm │ │ ├── find-co_occ.py │ │ ├── make-masks.py │ │ ├── make-mips.ijm │ │ ├── measure_clusters.py │ │ ├── particles-filter-3d.ijm │ │ └── run-cellpose.py │ ├── nCells-boyden │ │ ├── README.md │ │ └── find-cells.ijm │ ├── neuron-length │ │ ├── bridgegaps.py │ │ └── workflow.py │ ├── peaks-yeast-profile │ │ ├── README.md │ │ └── peaks_yeasts.ijm │ ├── pseudo-fix-diameterJ │ │ └── DiameterJ_1.ijm │ ├── radial-profiler │ │ ├── draw_points.py │ │ ├── englobing_circles.py │ │ ├── radial-profile.py │ │ └── rapport-radial-profile.md │ ├── segntrack │ │ ├── attempts │ │ │ ├── buildFocusCurve.py │ │ │ ├── classifier-max.classifier │ │ │ ├── classifier-std-dev.classifier │ │ │ ├── clean-labkit.ijm │ │ │ ├── extract-z-plots.ijm │ │ │ ├── labelling-std-dev.labeling │ │ │ ├── make_training_serie.py │ │ │ ├── max-proj.labeling │ │ │ ├── segmentation-script.ijm │ │ │ ├── set3 │ │ │ │ ├── iter1.classifier │ │ │ │ ├── iter1.labeling │ │ │ │ ├── iter2.classifier │ │ │ │ └── iter2.labeling │ │ │ ├── step-6.classifier │ │ │ └── try-3 │ │ │ │ ├── iteration-2.labeling │ │ │ │ ├── iteration-5.labeling │ │ │ │ ├── iteration-7.labeling │ │ │ │ ├── iteration-9.labeling │ │ │ │ └── new-try-classifier.classifier │ │ └── final │ │ │ ├── Doxyfile │ │ │ ├── Seg_N_Track.py │ │ │ ├── aggregateJSON.py │ │ │ └── nucleiClassifier.classifier │ ├── signal-rep-bacilli │ │ ├── README.md │ │ ├── macros │ │ │ └── toolsets │ │ │ │ └── Measure bacilli.ijm │ │ └── plugins │ │ │ ├── bacilli_measure.py │ │ │ └── bacilli_segment.py │ ├── spots-in-yeasts │ │ ├── build_training_set.py │ │ ├── cells-and-spots.py │ │ ├── detect-spots-attempt.py │ │ └── spots_in_yeasts.py │ ├── spots_in_neurites │ │ ├── Neurons_Spots.ijm │ │ ├── README.md │ │ ├── SIN_About.py │ │ ├── SIN_Check_MIP.py │ │ ├── SIN_Check_Segmentation.py │ │ ├── SIN_Check_Spots.py │ │ ├── SIN_Clear_Settings.py │ │ ├── SIN_Focus_Detection_MIP.py │ │ ├── SIN_Segmentation.py │ │ ├── SIN_Settings.py │ │ ├── SIN_Spot_Neurons.py │ │ ├── SIN_Thanks.py │ │ ├── SIN_Tips.py │ │ ├── Verif_Segmentation.ijm │ │ └── Verif_Spots.ijm │ ├── staining-fusion-ratio │ │ └── fusion-and-measure.py │ ├── track-n-measure-spots │ │ ├── keep-labels.ijm │ │ └── track-spots.ijm │ ├── utils │ │ ├── count-nuclei.py │ │ ├── expand-polygons.py │ │ ├── make-mips.ijm │ │ └── run-cellpose.py │ └── yeast-radial-profile │ │ └── radial-profile.py ├── packages │ ├── clean.sh │ ├── mdYeasts │ │ ├── __init__.py │ │ ├── makeNGon.py │ │ ├── makeSegmentation.py │ │ └── userIO.py │ ├── movingNgon │ │ ├── __init__.py │ │ ├── basicContours.py │ │ ├── basicOps.py │ │ ├── movingNgon.py │ │ └── rays.py │ ├── mriGeneral │ │ ├── RandomLUT.py │ │ └── __init__.py │ ├── nucleiTools │ │ ├── CountNuclei.py │ │ └── __init__.py │ └── spotsInNeurites │ │ ├── __init__.py │ │ └── settingsManager.py ├── stand-alones │ ├── README.md │ ├── astrocytesBloodVessels │ │ ├── ##old## │ │ │ ├── imageMapping.py │ │ │ └── incidenceMatrix.py │ │ ├── featuresFromIsosurface.py │ │ └── generateBlenderFile.py │ ├── blender │ │ └── materialToScript.py │ └── common-co-occ │ │ └── common-co-occ.py └── toolsets │ ├── count-cells │ └── Count Nuclei.ijm │ ├── general │ └── Random LUT.ijm │ ├── lls_transform_fiji │ ├── README.md │ ├── jars │ │ └── Lib │ │ │ └── lls_transform │ │ │ ├── __init__.py │ │ │ └── lls_transform.py │ ├── macros │ │ └── toolsets │ │ │ └── LLS Transforms.ijm │ └── plugins │ │ └── lls_transforms │ │ ├── lls_calib.py │ │ ├── lls_cgt.py │ │ ├── lls_deskew.py │ │ └── lls_measure.py │ ├── md_yeasts │ └── MD Yeasts.ijm │ ├── spots-in-neurites │ └── MIP And Spots.ijm │ └── spots_in_neurites │ └── Spots in neurites.ijm ├── elodie ├── environment.yml ├── genertae_pyramid.py ├── google3fc818bd9ad33039.md ├── leo ├── macros │ ├── detect-spots.ijm │ ├── measure-intensity-in-nucleus.ijm │ ├── stack-focus_mip.ijm │ ├── verif-masks-spots.ijm │ └── verif_mip.ijm ├── plugins │ ├── Create_Color_Palette.jar │ └── MRI_Roi_To_Line │ │ ├── MRI_Roi_To_Line.java │ │ └── RoiToLineTool.java └── toolsets │ ├── Cell_Transmigration │ └── cell_transmigration_analysis.ijm │ ├── Worm_Analyse │ ├── worm_segmentation.ijm │ └── worm_untangling.py │ ├── count_spines_on_dendrite │ └── Count_Spines_On_Dendrite.ijm │ └── opera_wellnames_from_CSV │ └── opera_wellnames_from_CSV.ijm ├── leslie └── macros │ └── Macro_Stitching.ijm ├── nicolas ├── draw_growth_cone_diagram.ijm └── toolsets │ ├── Muli_Scale_Blob_Detection.py │ ├── genertae_pyramid.py │ ├── growth_cone_diagram │ └── draw_growth_cone_diagram.ijm │ ├── growth_cone_visualization │ └── draw_growth_cone_diagram.ijm │ └── wavelet_transform_analysis.py ├── renaud ├── binning_large_dataset │ ├── README.md │ └── _binning.txt └── crop_large_dataset │ ├── README.md │ └── _crop.txt ├── sitemap.xml ├── sylvain ├── Macros │ ├── Coloc_Tools │ │ ├── Himanshu_2colors_V11_.ijm │ │ └── Himanshu_3colors_V10.ijm │ ├── Merge_Tools │ │ ├── Merge_2or3Colors_MDA_multipos_V1.ijm │ │ ├── Merge_trans-Cy5_MDA_time-positions_V1.ijm │ │ ├── README.md │ │ └── infos.txt │ ├── MuVi_SPIM_Convert_MIP_Tools │ │ ├── MuVi-SPIM_Convert_Tools_VersionF.ijm │ │ ├── README.md │ │ └── wiki_images │ │ │ ├── 1.montage.PNG │ │ │ └── 2.SaveAs.PNG │ └── Pombe_Tools │ │ ├── Pombe_Dots_V4.ijm │ │ ├── README.md │ │ └── infos.txt └── Toolsets │ ├── Convert_Tools.ijm │ ├── Convert_Tools.txt │ └── README.md ├── virginie └── macros │ ├── batch of ratiometric FRET using IO settings.ijm │ └── dynamic of focal ahesion.ijm └── volker ├── macros ├── Spinning_Disk_Make_Hyperstack_Batch.ijm ├── analyze_mt_polimerization.ijm ├── analyze_wheat_ear.ijm ├── area_of_tracked_objects.ijm ├── batch_coloc_biop_jacop.ijm ├── batch_concatenate_images.ijm ├── batch_convert_nd2_2_tif.ijm ├── batch_mip_projection.ijm ├── concatenate_tracks.ijm ├── convolve_plot.ijm ├── count_rosettes.ijm ├── count_stained_cells.ijm ├── discrete_histogram_entropy_.ijm ├── download_md_image_links.ijm ├── draw3D_data.ijm ├── export_RGB_And_Channels.ijm ├── export_czi_channels.ijm ├── export_rois_as_images.ijm ├── fwhm.ijm ├── ims2tif.ijm ├── measure_all_channels_on_frame.ijm ├── mri-updater.ijm ├── multi_stack_reg │ └── multi_stack_reg.ijm ├── normalize_image.ijm ├── rename_field.ijm ├── rename_files.ijm ├── replace_channel.ijm ├── restore_images.ijm ├── select_object_in_row.ijm ├── split_fields.ijm └── standardize_image.ijm ├── notebooks ├── .ipynb_checkpoints │ └── Adipocytes_Tools-checkpoint.ipynb ├── Adipocytes_Tools.ipynb └── ijmpy_unit_test.ipynb ├── plugins ├── filament_tracer │ ├── analysis │ │ ├── .svn │ │ │ ├── entries │ │ │ ├── prop-base │ │ │ │ ├── CorrelationCalculator.java.svn-base │ │ │ │ ├── GLCMTextureAnalyzer.java.svn-base │ │ │ │ └── ThresholdFinderUtil.java.svn-base │ │ │ └── text-base │ │ │ │ ├── CorrelationCalculator.java.svn-base │ │ │ │ ├── GLCMTextureAnalyzer.java.svn-base │ │ │ │ └── ThresholdFinderUtil.java.svn-base │ │ ├── GLCMTextureAnalyzer.java │ │ ├── ThresholdFinderUtil.java │ │ ├── clustering │ │ │ ├── .svn │ │ │ │ ├── entries │ │ │ │ ├── prop-base │ │ │ │ │ ├── FuzzyCMeansClustering.java.svn-base │ │ │ │ │ ├── FuzzyCMeansClusteringByte.java.svn-base │ │ │ │ │ ├── FuzzyCMeansClusteringFloat.java.svn-base │ │ │ │ │ ├── FuzzyCMeansClusteringInt.java.svn-base │ │ │ │ │ └── FuzzyCMeansClusteringShort.java.svn-base │ │ │ │ └── text-base │ │ │ │ │ ├── FuzzyCMeansClustering.java.svn-base │ │ │ │ │ ├── FuzzyCMeansClusteringByte.java.svn-base │ │ │ │ │ ├── FuzzyCMeansClusteringFloat.java.svn-base │ │ │ │ │ ├── FuzzyCMeansClusteringInt.java.svn-base │ │ │ │ │ └── FuzzyCMeansClusteringShort.java.svn-base │ │ │ ├── FuzzyCMeansClustering.java │ │ │ ├── FuzzyCMeansClusteringByte.java │ │ │ ├── FuzzyCMeansClusteringFloat.java │ │ │ ├── FuzzyCMeansClusteringInt.java │ │ │ └── FuzzyCMeansClusteringShort.java │ │ └── signalToNoise │ │ │ ├── .svn │ │ │ ├── entries │ │ │ ├── prop-base │ │ │ │ ├── MedianThresholdSignalToNoiseEstimator.java.svn-base │ │ │ │ ├── MedianThresholdSignalToNoiseEstimatorByte.java.svn-base │ │ │ │ ├── MedianThresholdSignalToNoiseEstimatorShort.java.svn-base │ │ │ │ ├── SignalToNoiseEstimator.java.svn-base │ │ │ │ ├── SignalToNoiseEstimatorByte.java.svn-base │ │ │ │ ├── SignalToNoiseEstimatorShort.java.svn-base │ │ │ │ ├── SignalToNoiseRatioCalculator.java.svn-base │ │ │ │ ├── SignalToNoiseRatioCalculatorByte.java.svn-base │ │ │ │ ├── SignalToNoiseRatioCalculatorFloat.java.svn-base │ │ │ │ ├── SignalToNoiseRatioCalculatorInt.java.svn-base │ │ │ │ └── SignalToNoiseRatioCalculatorShort.java.svn-base │ │ │ └── text-base │ │ │ │ ├── MedianThresholdSignalToNoiseEstimator.java.svn-base │ │ │ │ ├── MedianThresholdSignalToNoiseEstimatorByte.java.svn-base │ │ │ │ ├── MedianThresholdSignalToNoiseEstimatorShort.java.svn-base │ │ │ │ ├── SignalToNoiseEstimator.java.svn-base │ │ │ │ ├── SignalToNoiseEstimatorByte.java.svn-base │ │ │ │ ├── SignalToNoiseEstimatorShort.java.svn-base │ │ │ │ ├── SignalToNoiseRatioCalculator.java.svn-base │ │ │ │ ├── SignalToNoiseRatioCalculatorByte.java.svn-base │ │ │ │ ├── SignalToNoiseRatioCalculatorFloat.java.svn-base │ │ │ │ ├── SignalToNoiseRatioCalculatorInt.java.svn-base │ │ │ │ └── SignalToNoiseRatioCalculatorShort.java.svn-base │ │ │ ├── MedianThresholdSignalToNoiseEstimator.java │ │ │ ├── MedianThresholdSignalToNoiseEstimatorByte.java │ │ │ ├── MedianThresholdSignalToNoiseEstimatorShort.java │ │ │ ├── SignalToNoiseEstimator.java │ │ │ ├── SignalToNoiseEstimatorByte.java │ │ │ ├── SignalToNoiseEstimatorShort.java │ │ │ ├── SignalToNoiseRatioCalculator.java │ │ │ ├── SignalToNoiseRatioCalculatorByte.java │ │ │ ├── SignalToNoiseRatioCalculatorFloat.java │ │ │ ├── SignalToNoiseRatioCalculatorInt.java │ │ │ └── SignalToNoiseRatioCalculatorShort.java │ ├── statistics │ │ ├── BasicStatistics.java │ │ ├── BasicStatisticsByte.java │ │ ├── BasicStatisticsDouble.java │ │ ├── BasicStatisticsFloat.java │ │ ├── BasicStatisticsInt.java │ │ ├── BasicStatisticsShort.java │ │ └── studentTTest │ │ │ ├── .svn │ │ │ ├── entries │ │ │ ├── prop-base │ │ │ │ ├── APMath.java.svn-base │ │ │ │ ├── DoubleValue.java.svn-base │ │ │ │ ├── GammaFunction.java.svn-base │ │ │ │ ├── IncompleteBetaIntegral.java.svn-base │ │ │ │ ├── NormalDistribution.java.svn-base │ │ │ │ ├── StudentTDistribution.java.svn-base │ │ │ │ ├── StudentTTest.java.svn-base │ │ │ │ └── TestStudentT.java.svn-base │ │ │ └── text-base │ │ │ │ ├── APMath.java.svn-base │ │ │ │ ├── DoubleValue.java.svn-base │ │ │ │ ├── GammaFunction.java.svn-base │ │ │ │ ├── IncompleteBetaIntegral.java.svn-base │ │ │ │ ├── NormalDistribution.java.svn-base │ │ │ │ ├── StudentTDistribution.java.svn-base │ │ │ │ ├── StudentTTest.java.svn-base │ │ │ │ └── TestStudentT.java.svn-base │ │ │ ├── APMath.java │ │ │ ├── DoubleValue.java │ │ │ ├── GammaFunction.java │ │ │ ├── IncompleteBetaIntegral.java │ │ │ ├── NormalDistribution.java │ │ │ ├── StudentTDistribution.java │ │ │ ├── StudentTTest.java │ │ │ └── TestStudentT.java │ ├── tracing │ │ ├── .svn │ │ │ ├── entries │ │ │ ├── prop-base │ │ │ │ ├── BiggestXComparator.java.svn-base │ │ │ │ ├── Edge.java.svn-base │ │ │ │ ├── FilamentTracer.java.svn-base │ │ │ │ ├── FindSkeletonPoints.java.svn-base │ │ │ │ ├── PointsDistanceComparator.java.svn-base │ │ │ │ ├── PointsDistanceYComparator.java.svn-base │ │ │ │ ├── SeedPointsFinder.java.svn-base │ │ │ │ ├── SeedPointsFinderByte.java.svn-base │ │ │ │ ├── SeedPointsFinderFloat.java.svn-base │ │ │ │ ├── SeedPointsFinderInt.java.svn-base │ │ │ │ ├── SeedPointsFinderShort.java.svn-base │ │ │ │ ├── SkeletonTreeTracer.java.svn-base │ │ │ │ ├── SmallestXComparator.java.svn-base │ │ │ │ ├── Tracing.java.svn-base │ │ │ │ ├── TracingsLengthComparator.java.svn-base │ │ │ │ ├── TracingsMeanIntensityComparator.java.svn-base │ │ │ │ ├── TracingsSNRComparator.java.svn-base │ │ │ │ ├── TracingsYDistanceComparator.java.svn-base │ │ │ │ ├── Tree.java.svn-base │ │ │ │ ├── TreeTracer.java.svn-base │ │ │ │ ├── TreeTracerOptions.java.svn-base │ │ │ │ ├── TreeTracerOptionsView.java.svn-base │ │ │ │ └── TreeTracerView.java.svn-base │ │ │ └── text-base │ │ │ │ ├── BiggestXComparator.java.svn-base │ │ │ │ ├── Edge.java.svn-base │ │ │ │ ├── FilamentTracer.java.svn-base │ │ │ │ ├── FindSkeletonPoints.java.svn-base │ │ │ │ ├── PointsDistanceComparator.java.svn-base │ │ │ │ ├── PointsDistanceYComparator.java.svn-base │ │ │ │ ├── SeedPointsFinder.java.svn-base │ │ │ │ ├── SeedPointsFinderByte.java.svn-base │ │ │ │ ├── SeedPointsFinderFloat.java.svn-base │ │ │ │ ├── SeedPointsFinderInt.java.svn-base │ │ │ │ ├── SeedPointsFinderShort.java.svn-base │ │ │ │ ├── SkeletonTreeTracer.java.svn-base │ │ │ │ ├── SmallestXComparator.java.svn-base │ │ │ │ ├── Tracing.java.svn-base │ │ │ │ ├── TracingsLengthComparator.java.svn-base │ │ │ │ ├── TracingsMeanIntensityComparator.java.svn-base │ │ │ │ ├── TracingsSNRComparator.java.svn-base │ │ │ │ ├── TracingsYDistanceComparator.java.svn-base │ │ │ │ ├── Tree.java.svn-base │ │ │ │ ├── TreeTracer.java.svn-base │ │ │ │ ├── TreeTracerOptions.java.svn-base │ │ │ │ ├── TreeTracerOptionsView.java.svn-base │ │ │ │ └── TreeTracerView.java.svn-base │ │ ├── BiggestXComparator.java │ │ ├── Edge.java │ │ ├── FilamentTracer.java │ │ ├── PointsDistanceComparator.java │ │ ├── PointsDistanceYComparator.java │ │ ├── SeedPointsFinder.java │ │ ├── SeedPointsFinderByte.java │ │ ├── SeedPointsFinderFloat.java │ │ ├── SeedPointsFinderInt.java │ │ ├── SeedPointsFinderShort.java │ │ ├── SkeletonTreeTracer.java │ │ ├── SmallestXComparator.java │ │ ├── Tracing.java │ │ ├── TracingsLengthComparator.java │ │ ├── TracingsMeanIntensityComparator.java │ │ ├── TracingsSNRComparator.java │ │ ├── TracingsYDistanceComparator.java │ │ ├── Tree.java │ │ ├── TreeTracerOptions.java │ │ └── TreeTracerOptionsView.java │ └── workspace │ │ └── FindSeedPoints.java ├── grow_regions │ └── Grow_Regions.java ├── io-settings │ ├── IOSettings-12 │ │ ├── META-INF │ │ │ └── MANIFEST.MF │ │ ├── fr │ │ │ └── cnrs │ │ │ │ └── mri │ │ │ │ └── macro │ │ │ │ └── io │ │ │ │ ├── IOSettings.java │ │ │ │ └── IOSettingsEditorView.java │ │ └── tests │ │ │ └── fr │ │ │ └── cnrs │ │ │ └── mri │ │ │ └── macro │ │ │ └── io │ │ │ └── IOSettingsTest.java │ └── Macro_IO_Settings.java ├── lib │ └── legacy │ │ ├── mri-base-lib │ │ ├── META-INF │ │ │ └── MANIFEST.MF │ │ └── fr │ │ │ └── cnrs │ │ │ └── mri │ │ │ ├── files │ │ │ ├── ChecksumCalculator.java │ │ │ ├── ConfigurableFileFilter.java │ │ │ ├── FileInformation.java │ │ │ ├── MD5.java │ │ │ ├── RemoteFile.java │ │ │ └── tests │ │ │ │ ├── ChecksumCalculatorTest.java │ │ │ │ ├── ConfigurableFileFilterTest.java │ │ │ │ ├── FileInformationTest.java │ │ │ │ ├── MD5Test.java │ │ │ │ └── RemoteFileTest.java │ │ │ ├── logging │ │ │ ├── Log.java │ │ │ ├── LogViewer.java │ │ │ ├── LogViewerView.java │ │ │ ├── StringListHandler.java │ │ │ ├── resources │ │ │ │ └── logomri1.jpg │ │ │ └── tests │ │ │ │ ├── LogTest.java │ │ │ │ ├── LogViewerTest.java │ │ │ │ ├── LogViewerViewTest.java │ │ │ │ └── StringListHandlerTest.java │ │ │ ├── mvc │ │ │ ├── OWSPModel.java │ │ │ └── tests │ │ │ │ └── OWSPModelTest.java │ │ │ ├── server │ │ │ ├── Server.java │ │ │ ├── ServerLink.java │ │ │ └── tests │ │ │ │ ├── ServerLinkTest.java │ │ │ │ └── ServerTest.java │ │ │ ├── testData │ │ │ ├── TestConfig.java │ │ │ └── TestImages.java │ │ │ ├── tests │ │ │ └── suite │ │ │ │ └── MRIBaseLibTests.java │ │ │ └── thread │ │ │ └── Stoppable.java │ │ ├── mri-comp-lib │ │ ├── META-INF │ │ │ └── MANIFEST.MF │ │ └── fr │ │ │ └── cnrs │ │ │ └── mri │ │ │ ├── dialog │ │ │ ├── ModalDialogKiller.java │ │ │ ├── ModalDialogKillerView.java │ │ │ ├── RemoteJFileChooser.java │ │ │ └── tests │ │ │ │ └── ModalDialogKillerTest.java │ │ │ ├── fileList │ │ │ ├── FolderOpenerProxy.java │ │ │ ├── ListEditor.java │ │ │ ├── ListEditorView.java │ │ │ ├── MRIFolderOpener.java │ │ │ └── tests │ │ │ │ ├── FolderOpenerProxyTest.java │ │ │ │ ├── ListEditorTest.java │ │ │ │ └── MRIFolderOpenerTest.java │ │ │ └── tests │ │ │ └── suite │ │ │ └── MRICompLibTests.java │ │ └── mri-util-lib │ │ ├── META-INF │ │ └── MANIFEST.MF │ │ └── fr │ │ └── cnrs │ │ └── mri │ │ └── util │ │ ├── AccessibilityProxy.java │ │ ├── DatabaseUtil.java │ │ ├── EncryptionUtil.java │ │ ├── FileUtil.java │ │ ├── FileWriterUtil.java │ │ ├── TextUtil.java │ │ ├── TimeAndDateUtil.java │ │ ├── config │ │ ├── AbstractConfiguration.java │ │ └── tests │ │ │ └── AbstractConfigurationTest.java │ │ ├── logging │ │ ├── LoggingUtil.java │ │ └── tests │ │ │ └── LoggingUtilTest.java │ │ ├── os │ │ ├── MacProxy.java │ │ ├── OperatingSystemProxy.java │ │ ├── UnixProxy.java │ │ ├── WindowsProxy.java │ │ └── tests │ │ │ ├── MacProxyTest.java │ │ │ ├── OperatingSystemProxyTest.java │ │ │ └── WindowProxyTest.java │ │ ├── testData │ │ ├── AccessibilityProxyTestSuper.java │ │ ├── PrivateObject.java │ │ ├── SubSubclass.java │ │ ├── Subclass.java │ │ └── WantToAccess.java │ │ └── tests │ │ ├── AccessibilityProxyTest.java │ │ ├── DatabaseUtilTest.java │ │ ├── EncryptionUtilTest.java │ │ ├── FileUtilTest.java │ │ ├── FileWriterUtilTest.java │ │ ├── TextUtilTest.java │ │ ├── TimeAndDateUtilTest.java │ │ └── suite │ │ └── MRIUtilLibTests.java ├── roi_converter_tools │ ├── MRI_Extrema.java │ ├── MRI_Roi_Converter.java │ └── roi │ │ └── RoiConverter.java └── selection-tools │ ├── MRI_Roi_Util.java │ ├── Readme.md │ └── roi_util_example.ijm ├── scripts ├── convert_Opera_To_Hyperstack.py ├── make_isotropic.py └── mri-updater.py └── toolsets ├── 3D-nuclei-clustering ├── 3D_nuclei_clustering.ijm ├── Readme.md ├── dbscan_clustering_3D.py └── nearest_neighbor_distances_3D.py ├── 3D_cyst_analyzer ├── 3D_cyst_analyzer.ijm ├── clean_labels.ijm ├── export_frames.ijm ├── import_meshes.py ├── propagate_labels.ijm ├── remove_labels_in_selection.ijm ├── remove_small_labels.ijm └── surfaces_to_mask.py ├── 3D_nuclei_segmentation ├── point_coords_to_rois.ijm └── surfaces_to_mask.py ├── 3D_spot_colocalization ├── 3D_spot_colocalization_.ijm ├── 3D_spot_nearest_neighbor.py └── 3D_spot_py_interface.py ├── FISH_spot_counter ├── FISH_Spot_Counter.ijm ├── convertImaris2Tif.ijm ├── convert_ICS_to_TIF.ijm └── count_spots.py ├── FLIM-FRET_Volume_Tool └── FLIM-FRET_Volume_Tool.ijm ├── Intensity_Ratio_Nuclei_Cytoplasm └── Intensity_Ratio_Nuclei_Cytoplasm.ijm ├── Track_Microtubules_Tool ├── MRI_Track_Microtubules_Tool.ijm └── microtubule-tracking.py ├── adipocyte_tools ├── Adipocyte_Tools.ijm └── Readme.md ├── analyze_actin_flow └── analyze_actin_flow.ijm ├── analyze_alignment_of_muscles ├── analyze_alignment_of_muscles_tool_.ijm └── analyze_alignment_of_muscles_tool_.py ├── analyze_calcium_signals_in_dendritic_spine ├── Readme.md └── analyze_calcium_signals_in_dendritic_spines.ijm ├── analyze_cardiomyocytes ├── Analyze_Cardiomyocytes.ijm ├── Readme.md └── directionality_batch.py ├── analyze_comets_tool ├── Readme.md ├── analyze_comets_tool.ijm └── analyze_density_of_comets_tool.ijm ├── analyze_complex-roots_tools ├── Readme.md └── analyze_complex_roots_tools.ijm ├── analyze_dynamic_zones ├── analyze_dynamic_zones.ijm ├── cross_correlation.py └── xcorr.py ├── analyze_roots_tool └── MRI_Analyze_Roots_Tool.ijm ├── analyze_spheroid_cell_invasion_in_3D_matrix ├── Analyze_Spheroid_Cell_Invasion_In_3D_Matrix.ijm └── Readme.md ├── analyze_spots_per_protoplast ├── Analyse_Spots_Per_Protoplast.ijm └── Readme.md ├── arabidopsis_seedlings_tool ├── Arabidopsis_Seedlings_Tool.ijm └── Readme.md ├── area_of_axonal_projections_tool └── mri_area_of_axonal_projections_tool.ijm ├── automatic_scale_spot_detection_tool ├── __init__.py ├── automatic_scale_spot_detection_tool.ijm ├── find_spots_in_scale_space.py ├── link_rois.py ├── link_rois_betweenscales.py ├── merge_overlapping_spots.py ├── spotnode.py └── unittests │ └── spotnode_tests.py ├── batch-piv └── batch-particle-image-velocimetry.ijm ├── cluster_analysis_of_nuclei ├── cluster_analysis_of_nuclei_tool.ijm ├── dbscan_clustering.py └── find_nearest_neighbors.py ├── cochlea_hair_cell_counting └── Cochlea_Hair_Cell_Counting.ijm ├── cochlea_tools ├── cochlea_tools.ijm └── segment_cochlea_.ijm ├── color_quantization_tools ├── color_quantization_tools.ijm ├── color_quantization_tools.py └── dbscan_color_quantization.py ├── compre_filament_bundles └── compare_filament_bundles.ijm ├── convert_nikon_ti_andor_to_hyperstack ├── MRI_Convert_Nikon_TI_Andor_To_Hyperstac.ijm ├── MRI_Convert_Nikon_TI_Andor_To_Hyperstac.py └── Readme.md ├── convert_opera_to_hyperstack ├── Convert_Opera_To_Hyperstack.ijm ├── Convert_Opera_To_Hyperstack.py └── Readme.md ├── copy_random_data_tool └── copy_random_data_tool.ijm ├── count_axonal_projections └── count_axonal_projections.ijm ├── count_satellites_tool ├── Readme.md └── count_satellites_tool.ijm ├── count_spot_populations_tool ├── Count_Spot_Populations_Tool.ijm ├── bessel_.ijm ├── plot_gaussians.ijm ├── results_table-clusterer.groovy ├── results_table-clusterer.py ├── scale_space.ijm ├── scale_space_hessian.ijm ├── scales_.ijm └── test_R_.py ├── create_synthetic_spots_tool ├── Readme.md └── create_synthetic_spots_tool.ijm ├── discrete_histogram_entropy └── discrete_histogram_entropy.ijm ├── distance_between_minima_tool └── Distance_Between_Minima_Tool.ijm ├── fibrosis_tool └── MRI_Fibrosis_Tool.ijm ├── filament_morphology_tool └── filament_morphology_tool.ijm ├── filament_tools └── filament_tools.ijm ├── find_and_subtract_background └── find_and_subtract_background.ijm ├── foci_per_nucleus ├── Readme.md └── foci_per_nucleus_tool.ijm ├── heights_of_surfaces_tool ├── Readme.md ├── heights_of_surfaces_tools.ijm └── heights_of_surfaces_visualization.ipynb ├── image_conversion_tools ├── MRI_Image_Conversion_Tools.ijm └── Readme.md ├── incucyte_exporter └── incucyte_exporter.ijm ├── intensity_per_nucleus_tool ├── Readme.md └── intensity_per_nucleus_tool.ijm ├── intensity_ratio_nuclei_cytoplasm └── Intensity_Ratio_Nuclei_Cytoplasm.ijm ├── lipid_droplets_tool └── mri_lipid_droplets_tool.ijm ├── load_corresponding_images ├── Readme.md └── load_corresponding_images.ijm ├── macrophage_counting └── 3D_macrophage_counting.ijm ├── mc_positions_in_cell_tool └── positions_in_cell_tool.ijm ├── measure-rois └── measure_rois.ijm ├── measure_border_and_spots_tool └── measure_border_and_spots_tool.ijm ├── measure_cell_surfaces └── Measure_Cell_Surfaces.ijm ├── measure_intensity_outside_nuclei └── dsdna.ijm ├── measure_intensity_without_spots ├── conversion.py ├── export_wells.py ├── jump_to_label.py ├── label_image_to_image.py ├── measure_intensity_without_spots.ijm ├── measure_without_spots.py ├── metadata.py ├── process.py ├── quantification.py ├── remove_background.py └── summarize_data.py ├── measure_molecular_clusters └── measure_molecular_clusters_tool.ijm ├── measure_nuclei_and_membranes └── measure_nuclei_and_membranes.ijm ├── measure_rosette_area_tool └── measure_rosette_area_tool.ijm ├── measure_wound_healing_coherency ├── Readme.md └── measure_wound_healing_coherency.ijm ├── merge_channels_cellomix_tool └── merge_channels_cellomix.ijm ├── molecules_and_amassments_tool ├── Readme.md └── molecules_and_amassements_tool.ijm ├── mri-skin-tools └── MRI_Skin_Tools.ijm ├── mri_DoG_filter └── MRI_DoG_Filter.ijm ├── mri_g-ratio_tools ├── MRI_g-ratio_tools.ijm └── Readme.md ├── mri_metrics_tool └── mri_metrics_tool_.ijm ├── mri_root_hair_tool ├── MRI_Root_Hair_Tool.ijm └── Readme.md ├── mri_spot_coloc └── mri_spot_coloc_tool.ijm ├── nd2Avi └── nd_2_avi.ijm ├── nd_convert_projection_and_overlay └── nd_convert_projection_and_overlay.ijm ├── nd_to_hyperstack ├── ND_to_Hyperstack.ijm └── Readme.md ├── ndpi_export_regions ├── Readme.md └── ndpi_export_regions.ijm ├── neurite_analyzer ├── detect_RNA_FISH_spots.py ├── detect_RNA_FISH_spots_multiple_images.py ├── import_3D_spots_from_bigquant.ijm ├── import_spots_from_bigquant.ijm ├── neurite_analyzer.ijm ├── select_data.ijm └── spot_number_plot_.py ├── normalize_z_intensities └── normalize_z_intensities.ijm ├── opera_exporter ├── opera_export_tools.ijm └── opera_export_tools.py ├── osteoclasts ├── MRI_Osteoclasts_Tools.ijm └── osteoclasts.ilp ├── ph_by_distance_from_root_tool └── ph_by_distance_from_root_tool.ijm ├── phase_contrast_cell_analysis_tool └── MRI - Phase Contrast Cell Analysis Tool.ijm ├── photo_conversion_analysis_tools └── MRI_Photo_Conversion_Analysis_Tools.ijm ├── plaques_orientation ├── analyze_plaque_directions.ijm └── plaques.ilp ├── plot_distributions_tool └── plot_distributions_tool.ijm ├── plot_tools └── plot_tools.ijm ├── positions_in_cell_multiple_cells └── positions_in_cell_tool_multiple_cells.ijm ├── positions_in_cell_tool └── positions_in_cell_tool.ijm ├── qualify_dab_tools └── qualify_dab_tools.ijm ├── radial_movement_analyzer ├── radial_movement_analyzer.ijm ├── radial_movement_analyzer.py └── radial_movement_analyzer2.py ├── random_selection_from_table_tool └── random_selection_from_table_tool.ijm ├── repair_deleted_images ├── repair_deleted_images.ijm └── repair_images_.ijm ├── restore_images └── restore_images.ijm ├── roi_converter_tools └── MRI_Roi_Converter_Tools.ijm ├── run_command_on_image_opened_event └── run_command_on_image_opened_event.ijm ├── sarcomere_distance_tool └── sarcomere_distance_tool.ijm ├── scale_and_merge_images └── scale_and_merge_images.ijm ├── scratch_assay └── MRI_Wound_Healing_Tool.ijm ├── spine_analyzer ├── Readme.md ├── add_dendrite.py ├── adjust_display_of_labels.py ├── attach_spines.py ├── debug.py ├── find_spine.py ├── measure_all_spines.py ├── measure_polyline_dist.py ├── measure_spines.py ├── neurons.py ├── print_max_spine_label.py ├── replace_label.py ├── segment_spine.py ├── segmentation.py ├── spine_analyzer.ijm ├── stackutil.py ├── track_dendrites.py ├── track_spines.py └── unittests │ ├── __init__.py │ ├── alltests_.py │ ├── neuronstest.py │ ├── segmentationtest.py │ ├── stackutilstest.py │ └── testdata.py ├── spiral_mosaic_tools ├── Batch_Process_Cellomics_Mosaics.bsh ├── Batch_Process_Cellomics_Timeseries_Mosaics.bsh ├── Create_Spiral_Image.bsh └── Readme.md ├── spot_distances_tool ├── filter_spots.ijm ├── find_nearest_neighbors.py └── spot_distances_tool.ijm ├── synthetic_nuclei_generator └── synthetic_nuclei_generator.ijm ├── synthetic_tracking_data_generator └── synthetic_tracking_data_generator.ijm ├── tensin_dynamic_tool ├── analyze_dynamic_zones.ijm └── tensin_dynamic_tool.ijm ├── time_reverse_hyperstack └── time_reverse_hyperstack.ijm ├── tracks_to_rois └── tracks_2_Rois.ijm ├── transfection_efficiency_tool ├── percentage_of_transfected_cells_tool.ijm └── transfection_efficiency_tool.ijm ├── tree_ring_segmentation ├── batch_invert_.ijm ├── color_deconv.py ├── extract_masks.py ├── groovy │ └── export_rois.groovy ├── mri_tree_ring_tools.ijm ├── pythonProject │ ├── qpath_convert_paths.py │ ├── tree_rings_prepare_data.ipynb │ └── tree_rings_unet.ipynb ├── radial_profile.ijm ├── radial_profile2.ijm ├── segment_bark.py ├── segment_trunk.py ├── select_input_images.ijm └── tree_rings.py ├── turgomap_tools └── Turgomap_Tools.ijm ├── width_measurement_tool ├── Readme.md ├── plot_derivative.ijm └── width_measurement_tool.ijm ├── width_profile_tools ├── line_mask_to_line_roi.ijm ├── medial_axis.py ├── plugins.config ├── remeasure_thickness.ijm ├── reverse_plot.ijm ├── select_centerline.ijm ├── 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