├── .DS_Store ├── .Rbuildignore ├── .Rprofile ├── .gitignore ├── .renvignore ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── R ├── .DS_Store ├── anndataUtils.R ├── cciaHelpers.R ├── cciaImage.R ├── cciaImageCollection.R ├── cciaImageSet.R ├── dockerHelpers.R ├── flowGatingSet.R ├── flowHelpers.R ├── forkedTasks.R ├── imagejUtils.R ├── jupyterKernelUtils.R ├── magickHelpers.R ├── multifileLabelPopUtils.R ├── napariUtils.R ├── plotHelpers.R ├── populationUtils.R ├── reactiveObject.R ├── reactivePersistentObject.R ├── reactivePersistentObjectCollection.R ├── reactivePersistentObjectSet.R ├── sshUtils.R ├── taskCore.R ├── taskLauncher.R ├── taskProcess.R ├── trackHelpers.R ├── typeHelpers.R └── zzz.R ├── README.Rmd ├── README.md ├── cecelia.Rproj ├── im ├── .DS_Store ├── cciaLogo.png └── examples │ ├── .DS_Store │ ├── 2D_spleen │ ├── .DS_Store │ ├── 1_create_project.png │ ├── 2_import_image.png │ ├── 3_assign_channels.png │ ├── 4_seg_cellpose.png │ ├── 4_seg_cellpose_params.png │ ├── 4_seg_donblo.png │ ├── 4_seg_donblo_params.png │ ├── 5_create_gatingset.png │ ├── 5_gating.png │ ├── 5_gating_image.png │ ├── 6_spatial_neighbours.png │ ├── 6_spatial_neighbours_image.png │ ├── 7_interactions_heat.png │ ├── 8_pop_clustering.png │ ├── 8_pop_clustering_UMAP.png │ ├── 8_pop_clustering_heat.png │ ├── 8_pop_clustering_image.png │ └── 8_pop_clustering_params.png │ ├── 3D_2P │ ├── .DS_Store │ ├── 1_create_project.png │ ├── 2_import_image.png │ ├── 3_assign_channels.png │ ├── 4_AF_drift_A.png │ ├── 4_AF_drift_B.png │ ├── 4_AF_drift_image.png │ ├── 5_seg_cellpose_A.png │ ├── 5_seg_cellpose_B.png │ ├── 5_seg_cellpose_image.png │ ├── 6_tracking_A.png │ ├── 6_tracking_B.png │ ├── 6_tracking_B_filters.png │ ├── 6_tracking_image.png │ ├── 7_HMM.png │ ├── 7_HMM_pop.png │ ├── 7_HMM_pop_image.png │ ├── 7_HMM_result.png │ ├── 7_HMM_space.png │ ├── 7_HMM_task.png │ └── 7_HMM_time.png │ └── 3D_LN │ ├── .DS_Store │ ├── 1_create_project.png │ ├── 2_import_image.png │ ├── 3_assign_channels.png │ ├── 4_seg_cellpose_DC.png │ ├── 4_seg_cellpose_T.png │ ├── 5_gating.png │ ├── 6_TRITC_contact.png │ ├── 6_spatial_clusters.png │ ├── 6_spatial_contacts.png │ ├── 6_spatial_napari.png │ └── depth_correction │ ├── CD69.FITC_corrected.png │ ├── CD69.FITC_original.png │ ├── TRITC_corrected.png │ ├── TRITC_original.png │ ├── gBT.CTV_corrected.png │ ├── gBT.CTV_original.png │ ├── gDT.CTDR_corrected.png │ └── gDT.CTDR_original.png ├── inst ├── .DS_Store ├── IJ │ ├── .DS_Store │ ├── __init__.py │ ├── ccia │ │ ├── .DS_Store │ │ ├── __init__$py.class │ │ ├── __init__.py │ │ ├── histoImProcessor$py.class │ │ ├── histoImProcessor.py │ │ ├── imProcessor.config │ │ ├── liveImProcessor.py │ │ ├── processors │ │ │ ├── __init__$py.class │ │ │ ├── __init__.py │ │ │ ├── correct3Ddrift.py │ │ │ ├── imageUtils$py.class │ │ │ ├── imageUtils.py │ │ │ ├── morphologicalFilters$py.class │ │ │ └── morphologicalFilters.py │ │ └── wrappers │ │ │ ├── __init__$py.class │ │ │ ├── __init__.py │ │ │ ├── bioformatsWrapper$py.class │ │ │ ├── bioformatsWrapper.py │ │ │ ├── segmentationWrapper$py.class │ │ │ ├── segmentationWrapper.py │ │ │ ├── trackingWrapper$py.class │ │ │ └── trackingWrapper.py │ ├── createFromSequence.py │ ├── createMIP.py │ ├── exportImage.py │ ├── runDonblo.py │ └── runDonblo_DEBUG.py ├── app │ ├── .DS_Store │ ├── cecelia-Linux.sh │ ├── cecelia-macOSX.command │ ├── constantsCore.R │ ├── global.R │ ├── helpers │ │ ├── .DS_Store │ │ ├── colourHelpers.R │ │ ├── jsHelpers.R │ │ ├── plotHelpers.R │ │ └── shinyHelpers.R │ ├── lib │ │ ├── .DS_Store │ │ ├── libsCore.R │ │ ├── libsFlow.R │ │ └── libsShiny.R │ ├── modules │ │ ├── .DS_Store │ │ ├── inputDefinitions │ │ │ ├── .DS_Store │ │ │ ├── behaviourAnalysis │ │ │ │ ├── clusterTracks.json │ │ │ │ ├── hmmStates.json │ │ │ │ └── hmmTransitions.json │ │ │ ├── cleanupImages │ │ │ │ ├── .DS_Store │ │ │ │ ├── afCorrect.json │ │ │ │ ├── afCorrect.tson │ │ │ │ ├── afCorrect.xson │ │ │ │ ├── afCorrectPreview.json │ │ │ │ ├── afDriftCorrect.json │ │ │ │ ├── applyFilter.json │ │ │ │ ├── avgCorrect.json │ │ │ │ ├── cellposeCorrect.json │ │ │ │ ├── crop.json │ │ │ │ ├── driftCorrect.json │ │ │ │ ├── filterPreview.json │ │ │ │ ├── n2vCorrect.json │ │ │ │ ├── registerImages.json │ │ │ │ ├── removeStripes.json │ │ │ │ ├── retrieve.json │ │ │ │ ├── slidingWindowCorrect.json │ │ │ │ └── timeDeltaCorrect.json │ │ │ ├── clustPopulations │ │ │ │ ├── leidenClustering.json │ │ │ │ ├── retrieve.json │ │ │ │ └── upload.json │ │ │ ├── clustRegions │ │ │ │ └── kmeansClust.json │ │ │ ├── gatePopulations │ │ │ │ ├── .DS_Store │ │ │ │ ├── applyAutospill.json │ │ │ │ └── createGatingSet.json │ │ │ ├── importFlow │ │ │ │ └── fcsRaw.json │ │ │ ├── importImages │ │ │ │ ├── cellToLocation.json │ │ │ │ ├── copy.json │ │ │ │ ├── ometiff.json │ │ │ │ ├── omezarr.json │ │ │ │ ├── remove.json │ │ │ │ ├── retrieve.json │ │ │ │ ├── splitIntoCores.json │ │ │ │ ├── splitIntoCoresPreview.json │ │ │ │ ├── splitSeries.json │ │ │ │ ├── tenxXenium.json │ │ │ │ ├── transferFrom.json │ │ │ │ └── upload.json │ │ │ ├── pixcl │ │ │ │ ├── applyClassifier.json │ │ │ │ ├── assignToPops.json │ │ │ │ ├── createCombinedImage.json │ │ │ │ ├── retrieve.json │ │ │ │ └── upload.json │ │ │ ├── segment │ │ │ │ ├── .DS_Store │ │ │ │ ├── .Rapp.history │ │ │ │ ├── binariseTracks.json │ │ │ │ ├── cellpose.json │ │ │ │ ├── createBranching.json │ │ │ │ ├── donblo.json │ │ │ │ ├── ilee.json │ │ │ │ ├── mesmer.json │ │ │ │ ├── morphoWatershed.json │ │ │ │ ├── retrieve.json │ │ │ │ ├── seedDetectPreview.json │ │ │ │ ├── stardist.json │ │ │ │ ├── testPreview.json │ │ │ │ └── upload.json │ │ │ ├── signalAnalysis │ │ │ │ └── findSignalPeaks.json │ │ │ ├── spatialAnalysis │ │ │ │ ├── cellClusters.json │ │ │ │ ├── cellClustersMeshes.json │ │ │ │ ├── cellContacts.json │ │ │ │ ├── cellContactsMeshes.json │ │ │ │ ├── cellNeighbours.json │ │ │ │ ├── cellRegions.json │ │ │ │ ├── cellRegionsStats.json │ │ │ │ ├── cellsToStructuresWO.json │ │ │ │ ├── distLeadingEdge.json │ │ │ │ ├── networkWeights.json │ │ │ │ ├── popsContainedInShapes.json │ │ │ │ ├── retrieve.json │ │ │ │ └── upload.json │ │ │ ├── template.json │ │ │ ├── tracking │ │ │ │ ├── bayesianTracking.json │ │ │ │ ├── retrieve.json │ │ │ │ ├── trackmate.json │ │ │ │ └── upload.json │ │ │ └── trainModels │ │ │ │ ├── generateTrainingImages.json │ │ │ │ └── trainN2V.json │ │ ├── managers │ │ │ ├── dataManager.R │ │ │ ├── flowPlotManager.R │ │ │ ├── imageViewerManager.R │ │ │ ├── inputManager.R │ │ │ ├── moduleManager.R │ │ │ ├── plotChartsManager.R │ │ │ ├── populationManager.R │ │ │ ├── projectManager.R │ │ │ ├── selectionManager.R │ │ │ ├── setManager.R │ │ │ ├── shapesManager.R │ │ │ ├── taskManager.R │ │ │ ├── uiManager.R │ │ │ └── viewerManager.R │ │ ├── server │ │ │ ├── .DS_Store │ │ │ ├── _trackingCorrectionServer.R │ │ │ ├── behaviourAnalysisServer.R │ │ │ ├── cleanupImagesServer.R │ │ │ ├── clustPopulationsServer.R │ │ │ ├── clustRegionsServer.R │ │ │ ├── createProjectServer.R │ │ │ ├── gatePopulationsServer.R │ │ │ ├── importFlowServer.R │ │ │ ├── importImagesServer.R │ │ │ ├── manageMetadataServer.R │ │ │ ├── pixelClassificationServer.R │ │ │ ├── plotChartsServer.R │ │ │ ├── plotClustersUMAPServer.R │ │ │ ├── plotFlowGatingServer.R │ │ │ ├── plotHeatmapsServer.R │ │ │ ├── plotInteractionHeatmapsServer.R │ │ │ ├── plotPopDensitiesServer.R │ │ │ ├── projectSettingsServer.R │ │ │ ├── segmentImagesServer.R │ │ │ ├── signalAnalysisServer.R │ │ │ ├── spatialAnalysisServer.R │ │ │ ├── trackingCorrectionServer.R │ │ │ ├── trackingImagesServer.R │ │ │ └── trainModelsServer.R │ │ └── ui │ │ │ ├── .DS_Store │ │ │ ├── _trackingCorrectionUI.R │ │ │ ├── behaviourAnalysisUI.R │ │ │ ├── cleanupImagesUI.R │ │ │ ├── clustPopulationsUI.R │ │ │ ├── clustRegionsUI.R │ │ │ ├── createProjectUI.R │ │ │ ├── flowPlotUI.R │ │ │ ├── gatePopulationsUI.R │ │ │ ├── imageViewerUI.R │ │ │ ├── importFlowUI.R │ │ │ ├── importImagesUI.R │ │ │ ├── manageMetadataUI.R │ │ │ ├── pixelClassificationUI.R │ │ │ ├── plotChartsUI.R │ │ │ ├── populationUI.R │ │ │ ├── projectSettingsUI.R │ │ │ ├── segmentImagesUI.R │ │ │ ├── setAttributesUI.R │ │ │ ├── setUI.R │ │ │ ├── shapesUI.R │ │ │ ├── signalAnalysisUI.R │ │ │ ├── spatialAnalysisUI.R │ │ │ ├── taskManagerUI.R │ │ │ ├── trackingCorrectionUI.R │ │ │ ├── trackingImagesUI.R │ │ │ └── trainModelsUI.R │ ├── server.R │ ├── sourcesCore.R │ ├── ui.R │ ├── utils │ │ ├── flowGatingPlot.R │ │ └── taskMonitorUtils.R │ ├── viewer │ │ ├── input.json │ │ └── output.json │ └── www │ │ ├── .DS_Store │ │ ├── JS │ │ ├── app.js │ │ └── shinyjsExtended.js │ │ ├── css │ │ └── dark_mode.css │ │ └── img │ │ └── ninja_stack.png ├── config.yml ├── custom.yml ├── modules │ ├── .DS_Store │ └── sources │ │ ├── .DS_Store │ │ ├── behaviourAnalysis.R │ │ ├── behaviourAnalysis │ │ ├── .DS_Store │ │ ├── clusterTracks.R │ │ ├── createPseudotime.R │ │ ├── hmmHybrid.R │ │ ├── hmmStates.R │ │ ├── hmmStatesNoiseFilter.R │ │ ├── hmmTransitions.R │ │ └── py │ │ │ ├── __pycache__ │ │ │ └── cluster_tracks.cpython-38.pyc │ │ │ ├── cluster_tracks.py │ │ │ └── create_pseudotime.py │ │ ├── cleanupImages.R │ │ ├── cleanupImages │ │ ├── .DS_Store │ │ ├── afCorrect.R │ │ ├── afCorrectPreview.R │ │ ├── afDriftCorrect.R │ │ ├── applyFilter.R │ │ ├── avgCorrect.R │ │ ├── cellposeCorrect.R │ │ ├── crop.R │ │ ├── driftCorrect.R │ │ ├── filterPreview.R │ │ ├── n2vCorrect.R │ │ ├── py │ │ │ ├── __pycache__ │ │ │ │ ├── af_drift_correct.cpython-38.pyc │ │ │ │ └── apply_filter.cpython-38.pyc │ │ │ ├── af_correct.py │ │ │ ├── af_drift_correct.py │ │ │ ├── apply_filter.py │ │ │ ├── avg_correct.py │ │ │ ├── cellpose_correct.py │ │ │ ├── crop.py │ │ │ ├── drift_correct.py │ │ │ ├── n2v_correct.py │ │ │ ├── register_images.py │ │ │ ├── remove_stripes.py │ │ │ ├── sliding_window_correct.py │ │ │ └── time_delta_correct.py │ │ ├── registerImages.R │ │ ├── removeStripes.R │ │ ├── resetImageInfo.R │ │ ├── retrieve.R │ │ ├── slidingWindowCorrect.R │ │ ├── timeDeltaCorrect.R │ │ └── updateImageInfo.R │ │ ├── clustPopulations.R │ │ ├── clustPopulations │ │ ├── .DS_Store │ │ ├── integrateClustering.R │ │ ├── leidenClustering.R │ │ ├── py │ │ │ ├── __pycache__ │ │ │ │ └── leiden_clust.cpython-38.pyc │ │ │ └── leiden_clust.py │ │ ├── resetImageInfo.R │ │ ├── retrieve.R │ │ ├── updateImageInfo.R │ │ └── upload.R │ │ ├── clustRegions.R │ │ ├── clustRegions │ │ └── kmeansClust.R │ │ ├── gatePopulations.R │ │ ├── gatePopulations │ │ ├── .DS_Store │ │ ├── .Rapp.history │ │ ├── applyAutospill.R │ │ ├── createFlowFrame.R │ │ ├── createGatingSet.R │ │ └── resetImageInfo.R │ │ ├── hpc.R │ │ ├── hpc │ │ ├── .DS_Store │ │ ├── cleanupTransferredImages.R │ │ ├── resetImageInfo.R │ │ ├── retrieve.R │ │ ├── retrieveCciaObj.R │ │ ├── rmDirs.R │ │ ├── rmFiles.R │ │ ├── tailFile.R │ │ ├── testConnection.R │ │ ├── updateCecelia.R │ │ ├── updateUserLibraries.R │ │ ├── upload.R │ │ └── uploadCciaObj.R │ │ ├── importFlow.R │ │ ├── importFlow │ │ └── fcsRaw.R │ │ ├── importImages.R │ │ ├── importImages │ │ ├── .DS_Store │ │ ├── cellToLocation.R │ │ ├── copy.R │ │ ├── createMip.R │ │ ├── cropImage.R │ │ ├── normaliseImage.R │ │ ├── ometiff.R │ │ ├── omezarr.R │ │ ├── py │ │ │ ├── change_pixel_type.py │ │ │ ├── createMIP.py │ │ │ ├── from_cellToLocation.py │ │ │ ├── from_tenx_xenium.py │ │ │ ├── import_from_sequence.py │ │ │ ├── import_segmentation.py │ │ │ ├── normalise_image.py │ │ │ ├── rescale_image.py │ │ │ ├── split_into_cores.py │ │ │ └── switch_dim_order.py │ │ ├── remove.R │ │ ├── rescaleImage.R │ │ ├── resetImageInfo.R │ │ ├── retrieve.R │ │ ├── splitIntoCores.R │ │ ├── splitIntoCoresPreview.R │ │ ├── splitSeries.R │ │ ├── tenxXenium.R │ │ ├── transferFrom.R │ │ ├── updateImageInfo.R │ │ └── upload.R │ │ ├── launchpad.R │ │ ├── launchpad │ │ ├── resetImageInfo.R │ │ ├── runCciaObj.R │ │ └── runCciaSet.R │ │ ├── mflux.R │ │ ├── mflux │ │ ├── backupProject.R │ │ ├── recoverProject.R │ │ ├── resetImageInfo.R │ │ ├── retrieveProject.R │ │ └── uploadProject.R │ │ ├── objcl.R │ │ ├── objcl │ │ ├── .DS_Store │ │ ├── .Rapp.history │ │ ├── applyClassifier.R │ │ ├── assignToPops.R │ │ ├── createCombinedImage.R │ │ ├── py │ │ │ ├── __pycache__ │ │ │ │ ├── apply_classifier.cpython-38.pyc │ │ │ │ ├── assign_to_pops.cpython-38.pyc │ │ │ │ ├── create_combined_image.cpython-38.pyc │ │ │ │ └── generate_training_images.cpython-38.pyc │ │ │ ├── apply_classifier.py │ │ │ ├── assign_to_pops.py │ │ │ └── create_combined_image.py │ │ ├── resetImageInfo.R │ │ ├── retrieve.R │ │ └── upload.R │ │ ├── pixcl.R │ │ ├── pixcl │ │ ├── .DS_Store │ │ ├── .Rapp.history │ │ ├── applyClassifier.R │ │ ├── assignToPops.R │ │ ├── createCombinedImage.R │ │ ├── py │ │ │ ├── __pycache__ │ │ │ │ ├── apply_classifier.cpython-38.pyc │ │ │ │ ├── assign_to_pops.cpython-38.pyc │ │ │ │ ├── create_combined_image.cpython-38.pyc │ │ │ │ └── generate_training_images.cpython-38.pyc │ │ │ ├── apply_classifier.py │ │ │ ├── assign_to_pops.py │ │ │ └── create_combined_image.py │ │ ├── resetImageInfo.R │ │ ├── retrieve.R │ │ └── upload.R │ │ ├── segment.R │ │ ├── segment │ │ ├── .DS_Store │ │ ├── binariseTracks.R │ │ ├── cellpose.R │ │ ├── createBranching.R │ │ ├── donblo.R │ │ ├── ilee.R │ │ ├── mesmer.R │ │ ├── morphoWatershed.R │ │ ├── py │ │ │ ├── .DS_Store │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── cellpose_wrapper.cpython-38.pyc │ │ │ │ ├── donblo.cpython-38.pyc │ │ │ │ ├── mesmer_wrapper.cpython-38.pyc │ │ │ │ ├── morpho_watershed.cpython-38.pyc │ │ │ │ ├── sd_wrapper.cpython-38.pyc │ │ │ │ ├── seed_based_watershed.cpython-38.pyc │ │ │ │ ├── stardist.cpython-38.pyc │ │ │ │ └── test_preview.cpython-38.pyc │ │ │ ├── binarise_tracks.py │ │ │ ├── cellpose_wrapper.py │ │ │ ├── create_branching.py │ │ │ ├── donblo.py │ │ │ ├── ilee_wrapper.py │ │ │ ├── mesmer_wrapper.py │ │ │ ├── morpho_watershed.py │ │ │ ├── sd_wrapper.py │ │ │ └── test_preview.py │ │ ├── resetImageInfo.R │ │ ├── retrieve.R │ │ ├── seedDetectPreview.R │ │ ├── stardist.R │ │ ├── testPreview.R │ │ ├── updateImageInfo.R │ │ └── upload.R │ │ ├── signalAnalysis.R │ │ ├── signalAnalysis │ │ ├── .DS_Store │ │ ├── findSignalPeaks.R │ │ └── py │ │ │ └── .DS_Store │ │ ├── spatialAnalysis.R │ │ ├── spatialAnalysis │ │ ├── .DS_Store │ │ ├── cellClusters.R │ │ ├── cellClustersMeshes.R │ │ ├── cellContacts.R │ │ ├── cellContactsMeshes.R │ │ ├── cellNeighbours.R │ │ ├── cellRegions.R │ │ ├── cellRegionsStats.R │ │ ├── cellsToStructuresWO.R │ │ ├── distLeadingEdge.R │ │ ├── networkWeights.R │ │ ├── popsContainedInShapes.R │ │ ├── py │ │ │ ├── __pycache__ │ │ │ │ ├── cell_clusters_mesh.cpython-38.pyc │ │ │ │ ├── cell_contacts_mesh.cpython-38.pyc │ │ │ │ └── cell_neighbours.cpython-38.pyc │ │ │ ├── cell_clusters_mesh.py │ │ │ ├── cell_contacts_mesh.py │ │ │ ├── cell_neighbours.py │ │ │ └── pops_contained_in_shapes.py │ │ ├── resetImageInfo.R │ │ ├── retrieve.R │ │ └── upload.R │ │ ├── taskTest.R │ │ ├── taskTest │ │ └── echo.R │ │ ├── tracking.R │ │ ├── tracking │ │ ├── .DS_Store │ │ ├── bayesianTracking.R │ │ ├── importTracking.R │ │ ├── py │ │ │ ├── __pycache__ │ │ │ │ └── bayesian_tracking.cpython-38.pyc │ │ │ └── bayesian_tracking.py │ │ ├── resetImageInfo.R │ │ ├── retrieve.R │ │ └── upload.R │ │ ├── trainModels.R │ │ └── trainModels │ │ ├── .DS_Store │ │ ├── generateTrainingImages.R │ │ ├── py │ │ ├── __pycache__ │ │ │ └── generate_training_images.cpython-38.pyc │ │ ├── generate_training_images.py │ │ └── train_n2v.py │ │ ├── resetImageInfo.R │ │ └── trainN2V.R ├── patches │ └── cellpose │ │ ├── core.py │ │ └── dynamics.py ├── py-env │ ├── .DS_Store │ ├── conda-env.yml │ ├── init-py-modules-image-nogui.txt │ └── requirements.txt ├── py │ ├── .DS_Store │ ├── ILEE_CSK │ │ ├── ILEE_matlab_3D.m │ │ ├── LICENSE.txt │ │ ├── README.md │ │ ├── __init__.py │ │ ├── fast_interp.py │ │ ├── functions.py │ │ └── test_directory.m │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-39.pyc │ │ ├── config_utils.cpython-39.pyc │ │ └── label_props_view.cpython-39.pyc │ ├── bayesian_tracking_utils.py │ ├── cellpose_utils.py │ ├── colormap_utils.py │ ├── colour_utils.py │ ├── config_utils.py │ ├── correction_utils.py │ ├── dim_utils.py │ ├── donblo_utils.py │ ├── ilee_utils.py │ ├── imagej_utils.py │ ├── label_props_utils.py │ ├── label_props_view.py │ ├── label_utils.py │ ├── local_peak_seeds_utils.py │ ├── logfile_utils.py │ ├── math_helpers.py │ ├── measure_utils.py │ ├── mesmer_utils.py │ ├── morpho_utils.py │ ├── morpho_watershed_utils.py │ ├── napari_utils.py │ ├── ome_xml_utils.py │ ├── opal_utils.py │ ├── points_utils.py │ ├── pop_utils.py │ ├── rapids_sc_utils.py │ ├── scanpy_utils.py │ ├── script_utils.py │ ├── seed_utils.py │ ├── segmentation_utils.py │ ├── shape_utils.py │ ├── sitkibex │ │ ├── .DS_Store │ │ ├── LICENSE │ │ ├── NOTICE │ │ ├── __init__.py │ │ ├── __main__.py │ │ ├── cli.py │ │ ├── globals.py │ │ ├── image_utilities.py │ │ ├── io.py │ │ ├── registration.py │ │ ├── registration_utilities.py │ │ ├── resample.py │ │ └── xml_info.py │ ├── slice_utils.py │ ├── stardist_utils.py │ ├── tiff_utils.py │ ├── tracking_utils.py │ ├── type_helpers.py │ └── zarr_utils.py ├── r-requirements.txt ├── scripts │ ├── .DS_Store │ └── hpc │ │ ├── .DS_Store │ │ └── slurm │ │ ├── installConda.slurm │ │ ├── updateCecelia.sh │ │ ├── updateUserLibraries.sh │ │ └── watchJobCompletion.sh └── templates │ ├── .DS_Store │ └── hpc │ ├── .DS_Store │ └── slurm │ ├── .DS_Store │ ├── hpcCPU.slurm.tpl │ ├── hpcGPU.slurm.tpl │ └── hpcWatchJob.tpl ├── man ├── .DS_Store ├── AnndataUtils.Rd ├── CciaImage.Rd ├── CciaImageCollection.Rd ├── CciaImageSet.Rd ├── FlowGatingSet.Rd ├── ImagejUtils.Rd ├── JupyterKernelUtils.Rd ├── MultifileLabelPopUtils.Rd ├── NapariUtils.Rd ├── PopulationUtils.Rd ├── ReactiveObject.Rd ├── ReactivePersistentObject.Rd ├── ReactivePersistentObjectCollection.Rd ├── ReactivePersistentObjectSet.Rd ├── SshUtils.Rd ├── TaskCore.Rd ├── TaskLauncher.Rd ├── TaskProcess.Rd └── dot-normDTCol.Rd ├── renv.lock ├── renv ├── .gitignore ├── activate.R └── settings.json ├── renv_4_4_x.lock ├── src └── .DS_Store ├── tests └── testthat.R └── vignettes ├── .DS_Store ├── XCR1rebuttal.Rmd ├── app ├── conditionalPanels.R ├── dynamicInput.R ├── dynamicUI.R ├── menuTabs.R ├── plotBlank.R ├── plotCharts.R ├── plotClustersUMAP.R ├── plotDensity.R ├── plotFlowGating.R ├── plotHeatmaps.R ├── plotInteractionHeatmaps.R ├── plotTrackClustersUMAP.R ├── sortInputs.R ├── trackManager.R ├── trackManager2.R ├── trackViewer.R ├── trackViewer2.R ├── trackViewer3.R ├── trackViewer3_.R ├── updateSortable.R ├── uploadFiles.R └── www ├── autospill.Rmd ├── backupProjects.Rmd ├── behaviourCD11c.Rmd ├── behaviourCML.Rmd ├── behaviourCornea.Rmd ├── behaviourDTx.Rmd ├── behaviourGCAMP.Rmd ├── behaviourGCAMP_all.Rmd ├── behaviourGCAMP_gBT_OTI.Rmd ├── behaviourGCAMP_gBT_TRITC.Rmd ├── behaviourGROOM.Rmd ├── behaviourH2Kb.Rmd ├── behaviourLymphaticVessels.Rmd 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