Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | V A apply_gaussian_smoothing() (in module cyto.postprocessing.sparse_to_sparse) B build_task_graph() (in module cyto.tasks.graph) C cache_exists() (in module cyto.utils.seg_cache) cal_kinematics() (in module cyto.utils.kinematics) cal_msd() (in module cyto.utils.kinematics) cal_viability() (in module cyto.postprocessing.sparse_to_sparse) calculate_cdi() (in module cyto.postprocessing.sparse_to_sparse) Cellpose (class in cyto.segmentation.cellpose) CellTriangulation (class in cyto.postprocessing.graph) ChannelMerge (class in cyto.utils.utils) check_gpu_memory() (in module cyto.utils.utils) compute_central_difference() (in module cyto.postprocessing.sparse_to_sparse) compute_moving_average() (in module cyto.postprocessing.sparse_to_sparse) compute_msd_time_lag() (in module cyto.utils.kinematics) compute_msd_track_vectorized() (in module cyto.utils.kinematics) compute_savgol_filter() (in module cyto.postprocessing.sparse_to_sparse) compute_smoothed_gradient() (in module cyto.postprocessing.sparse_to_sparse) create_trackmate_model() (cyto.tracking.trackmate_in_mem.TrackMateInMemoryProcessor method) CrossCellContactMeasures (class in cyto.postprocessing.graph) CrossChannelCorrelation (class in cyto.preprocessing.cross_channel_correlation) CrossTableOperation (class in cyto.postprocessing.sparse_to_sparse) cyto.postprocessing.graph module cyto.postprocessing.interaction_detection module cyto.postprocessing.plots.network module cyto.postprocessing.plots.timeseries module cyto.postprocessing.sparse_to_dense module cyto.postprocessing.sparse_to_sparse module cyto.preprocessing.cross_channel_correlation module cyto.preprocessing.denosing module cyto.preprocessing.flat_field_correction module cyto.preprocessing.normalization module cyto.runners.base module cyto.runners.container_worker module cyto.runners.docker module cyto.runners.singularity module cyto.segmentation.base module cyto.segmentation.cellpose module cyto.segmentation.stardist module cyto.tasks.base module cyto.tasks.definitions module cyto.tasks.graph module cyto.tasks.manager module cyto.tracking.trackmate module cyto.tracking.trackmate_in_mem module cyto.tracking.trackpy module cyto.utils.config module cyto.utils.kinematics module cyto.utils.label_to_table module cyto.utils.seg_cache module cyto.utils.utils module D dependencies (cyto.tasks.definitions.Task attribute) DetectInteractions (class in cyto.postprocessing.interaction_detection) distance() (in module cyto.postprocessing.interaction_detection) DockerRunner (class in cyto.runners.docker) draw_network_with_clustering() (in module cyto.postprocessing.plots.network) E execute() (cyto.tasks.manager.TaskManager method) execution_config (cyto.tasks.definitions.Task attribute) export_tracking_results() (cyto.tracking.trackmate_in_mem.TrackMateInMemoryProcessor method) extract_segment_features() (in module cyto.utils.label_to_table) F FeatureFilter (class in cyto.postprocessing.sparse_to_sparse) fit_model() (in module cyto.postprocessing.sparse_to_sparse) G GammaCorrection (class in cyto.preprocessing.normalization) gaussian_kernel() (in module cyto.postprocessing.sparse_to_sparse) get_cache_filename() (in module cyto.utils.seg_cache) get_execution_order() (in module cyto.tasks.graph) get_task_by_name() (in module cyto.tasks.graph) get_task_result() (cyto.tasks.manager.TaskManager method) get_task_results() (cyto.tasks.manager.TaskManager method) H hex_to_rgb() (in module cyto.postprocessing.plots.network) I ImageToLabel (class in cyto.utils.utils) instance (cyto.tasks.definitions.Task attribute) intensity_norm() (in module cyto.postprocessing.sparse_to_sparse) intensity_norm_percentile() (in module cyto.postprocessing.sparse_to_sparse) K KernelDensityEstimation (class in cyto.postprocessing.sparse_to_dense) L label_centroids_to_pointlist_sitk() (in module cyto.postprocessing.graph) label_to_sparse() (in module cyto.utils.label_to_table) labels_to_spots_csv() (cyto.tracking.trackmate_in_mem.TrackMateInMemoryProcessor method) left_table_merge() (in module cyto.postprocessing.sparse_to_sparse) load_db_config() (in module cyto.utils.config) load_notebook_config() (in module cyto.utils.config) load_segmentation_cache() (in module cyto.utils.seg_cache) load_tiff_data() (cyto.tracking.trackmate_in_mem.TrackMateInMemoryProcessor method) M main() (in module cyto.runners.container_worker) (in module cyto.tracking.trackmate) merge_dicts() (in module cyto.utils.label_to_table) model_func() (in module cyto.postprocessing.sparse_to_sparse) module cyto.postprocessing.graph cyto.postprocessing.interaction_detection cyto.postprocessing.plots.network cyto.postprocessing.plots.timeseries cyto.postprocessing.sparse_to_dense cyto.postprocessing.sparse_to_sparse cyto.preprocessing.cross_channel_correlation cyto.preprocessing.denosing cyto.preprocessing.flat_field_correction cyto.preprocessing.normalization cyto.runners.base cyto.runners.container_worker cyto.runners.docker cyto.runners.singularity cyto.segmentation.base cyto.segmentation.cellpose cyto.segmentation.stardist cyto.tasks.base cyto.tasks.definitions cyto.tasks.graph cyto.tasks.manager cyto.tracking.trackmate cyto.tracking.trackmate_in_mem cyto.tracking.trackpy cyto.utils.config cyto.utils.kinematics cyto.utils.label_to_table cyto.utils.seg_cache cyto.utils.utils module (cyto.tasks.definitions.Task attribute) N name (cyto.tasks.definitions.Task attribute) O OPS (cyto.postprocessing.sparse_to_sparse.FeatureFilter attribute) P params (cyto.tasks.definitions.Task attribute) PercentileNormalization (class in cyto.preprocessing.normalization) PipelineTask (class in cyto.tasks.base) pixelwise_correlation() (in module cyto.preprocessing.cross_channel_correlation) plot_centrality_boxplots_by_timepoint() (in module cyto.postprocessing.plots.timeseries) plot_centrality_histograms() (in module cyto.postprocessing.plots.timeseries) plot_clustering_boxplots_by_timepoint() (in module cyto.postprocessing.plots.timeseries) plot_clustering_histograms() (in module cyto.postprocessing.plots.timeseries) plot_contact_vs_time() (in module cyto.postprocessing.plots.timeseries) plot_network_centrality() (in module cyto.postprocessing.plots.network) R run() (cyto.runners.base.RunnerBase method) (cyto.runners.docker.DockerRunner method) (cyto.runners.singularity.SingularityRunner method) run_baremetal() (cyto.segmentation.base.SegmentationBase method) (cyto.tasks.base.PipelineTask method) run_container() (cyto.segmentation.base.SegmentationBase method) (cyto.segmentation.cellpose.Cellpose method) (cyto.tasks.base.PipelineTask method) run_single_frame() (cyto.postprocessing.graph.CrossCellContactMeasures method) run_tracking() (cyto.tracking.trackmate_in_mem.TrackMateInMemoryProcessor method) run_trackmate_on_data() (in module cyto.tracking.trackmate_in_mem) RunnerBase (class in cyto.runners.base) S save_segmentation_cache() (in module cyto.utils.seg_cache) SegmentationBase (class in cyto.segmentation.base) SingularityRunner (class in cyto.runners.singularity) StarDist (class in cyto.segmentation.stardist) T tags (cyto.tasks.definitions.Task attribute) Task (class in cyto.tasks.definitions) TaskManager (class in cyto.tasks.manager) TrackMate (class in cyto.tracking.trackmate) TrackMateInMemoryProcessor (class in cyto.tracking.trackmate_in_mem) V VideoInteractions (class in cyto.postprocessing.interaction_detection) visualize_segmentations() (in module cyto.postprocessing.plots.network)