API Reference

• cyto.preprocessing
  • GammaCorrection
  • PercentileNormalization
  • CrossChannelCorrelation
  • pixelwise_correlation()
• cyto.segmentation
  • SegmentationBase
  • StarDist
  • Cellpose
• cyto.tracking
  • TrackMate
  • main()
  • TrackMateInMemoryProcessor
  • run_trackmate_on_data()
• cyto.postprocessing
  • DetectInteractions
  • VideoInteractions
  • distance()
  • CellTriangulation
  • CrossCellContactMeasures
  • label_centroids_to_pointlist_sitk()
  • CrossTableOperation
  • FeatureFilter
  • apply_gaussian_smoothing()
  • cal_viability()
  • calculate_cdi()
  • compute_central_difference()
  • compute_moving_average()
  • compute_savgol_filter()
  • compute_smoothed_gradient()
  • fit_model()
  • gaussian_kernel()
  • intensity_norm()
  • intensity_norm_percentile()
  • left_table_merge()
  • model_func()
  • KernelDensityEstimation
  • cyto.postprocessing.plots.timeseries
  • plot_centrality_boxplots_by_timepoint()
  • plot_centrality_histograms()
  • plot_clustering_boxplots_by_timepoint()
  • plot_clustering_histograms()
  • plot_contact_vs_time()
  • cyto.postprocessing.plots.network
  • draw_network_with_clustering()
  • hex_to_rgb()
  • plot_network_centrality()
  • visualize_segmentations()
• cyto.utils
  • load_db_config()
  • load_notebook_config()
  • ChannelMerge
  • ImageToLabel
  • check_gpu_memory()
  • extract_segment_features()
  • label_to_sparse()
  • merge_dicts()
  • cal_kinematics()
  • cal_msd()
  • compute_msd_time_lag()
  • compute_msd_track_vectorized()
  • cyto.utils.seg_cache
  • cache_exists()
  • get_cache_filename()
  • load_segmentation_cache()
  • save_segmentation_cache()
• cyto.runners
  • RunnerBase
  • DockerRunner
  • SingularityRunner
  • main()
• cyto.tasks
  • PipelineTask
  • Task
  • build_task_graph()
  • get_execution_order()
  • get_task_by_name()
  • TaskManager