Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y A access_key_id (ContextConfig attribute) account (ContextConfig attribute), [1] B bandwidth (ParametersConfigFeatureDistributions attribute), [1] (ParametersConfigMetricsDistributions attribute) bin_to_hex() (in module cell_abm_pipeline.tasks.bin_to_hex) binary (ParametersConfigImages attribute) bins (ParametersConfig attribute) bounding_box (ParametersConfig attribute) bounds (ParametersConfigFeatureDistributions attribute), [1] (ParametersConfigMetricsDistributions attribute) box (ParametersConfigColonyContours attribute) (ParametersConfigColorizer attribute) (ParametersConfigImages attribute) (ParametersConfigMeshes attribute) (ParametersConfigProjections attribute) (ParametersConfigScan attribute) (ParametersConfigShapeAverage attribute) (ParametersConfigShapeContours attribute) (ParametersConfigShapeModes attribute) (ParametersConfigSimulariumObjects attribute) (ParametersConfigSimulariumShapes attribute) box_size (ParametersConfig attribute) build_svg_image() (in module cell_abm_pipeline.tasks.build_svg_image) C calculate (ParametersConfig attribute) calculate_category_durations() (in module cell_abm_pipeline.tasks.calculate_category_durations) calculate_data_bins() (in module cell_abm_pipeline.tasks.calculate_data_bins) Calculation (class in cell_abm_pipeline.flows.run_fargate_calculations) categories (ParametersConfigObjectStorage attribute), [1] cell_abm_pipeline.flows module cell_abm_pipeline.flows.analyze_basic_metrics module cell_abm_pipeline.flows.analyze_cell_shapes module cell_abm_pipeline.flows.analyze_colony_dynamics module cell_abm_pipeline.flows.calculate_coefficients module cell_abm_pipeline.flows.calculate_image_properties module cell_abm_pipeline.flows.calculate_neighbors module cell_abm_pipeline.flows.calculate_positions module cell_abm_pipeline.flows.calculate_properties module cell_abm_pipeline.flows.convert_arcade_format module cell_abm_pipeline.flows.convert_physicell_format module cell_abm_pipeline.flows.demo module cell_abm_pipeline.flows.download_images module cell_abm_pipeline.flows.generate_voronoi_tessellation module cell_abm_pipeline.flows.group_basic_metrics module cell_abm_pipeline.flows.group_cell_shapes module cell_abm_pipeline.flows.group_colony_dynamics module cell_abm_pipeline.flows.group_resource_usage module cell_abm_pipeline.flows.initialize_arcade_simulations module cell_abm_pipeline.flows.initialize_physicell_simulations module cell_abm_pipeline.flows.make_simulation_movies module cell_abm_pipeline.flows.organize_calculation_files module cell_abm_pipeline.flows.parse_arcade_simulations module cell_abm_pipeline.flows.parse_physicell_simulations module cell_abm_pipeline.flows.plot_basic_metrics module cell_abm_pipeline.flows.plot_cell_shapes module cell_abm_pipeline.flows.plot_colony_dynamics module cell_abm_pipeline.flows.plot_resource_usage module cell_abm_pipeline.flows.process_sample module cell_abm_pipeline.flows.run_batch_simulations module cell_abm_pipeline.flows.run_docker_simulations module cell_abm_pipeline.flows.run_fargate_calculations module cell_abm_pipeline.flows.sample_image module cell_abm_pipeline.flows.summarize_manifest module cell_abm_pipeline.tasks module cell_abm_pipeline.tasks.bin_to_hex module cell_abm_pipeline.tasks.build_svg_image module cell_abm_pipeline.tasks.calculate_category_durations module cell_abm_pipeline.tasks.calculate_data_bins module cell_abm_pipeline.tasks.check_data_bounds module cell_abm_pipeline.tasks.make_bar_figure module cell_abm_pipeline.tasks.make_box_figure module cell_abm_pipeline.tasks.make_centroids_figure module cell_abm_pipeline.tasks.make_contour_figure module cell_abm_pipeline.tasks.make_density_figure module cell_abm_pipeline.tasks.make_graph_figure module cell_abm_pipeline.tasks.make_heatmap_figure module cell_abm_pipeline.tasks.make_histogram_figure module cell_abm_pipeline.tasks.make_line_figure module cell_abm_pipeline.tasks.make_range_figure module cell_abm_pipeline.tasks.make_scatter_figure module cell_abm_pipeline.tasks.physicell module cell_colors (ParametersConfig attribute) cell_height (ParametersConfig attribute) cell_volume (ParametersConfig attribute) cells_per_fov (ParametersConfig attribute) centroids (ParametersConfig attribute) channel (ParametersConfig attribute), [1] channels (ParametersConfig attribute) check_data_bounds() (in module cell_abm_pipeline.tasks.check_data_bounds) chunk (ParametersConfig attribute), [1], [2] chunk_size (ParametersConfigColorizer attribute) (ParametersConfigImages attribute) clean_jobs (ParametersConfig attribute), [1] cluster (ContextConfig attribute) COEFFICIENTS (Calculation attribute) colony_contours (ParametersConfig attribute) colorizer (ParametersConfig attribute) colormaps (ParametersConfigNeighborPositions attribute) colors (ParametersConfigShapeModes attribute) (ParametersConfigVarianceExplained attribute) components (ParametersConfig attribute) (ParametersConfigFeatureComponents attribute) (ParametersConfigFeatureCorrelations attribute), [1] (ParametersConfigFeatureDistributions attribute), [1] (ParametersConfigModeCorrelations attribute), [1] (ParametersConfigShapeAverage attribute) (ParametersConfigShapeModes attribute), [1] (ParametersConfigVarianceExplained attribute), [1] conditions (SeriesConfig attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] contact_sheet (ParametersConfig attribute), [1], [2] ContextConfig (class in cell_abm_pipeline.flows.analyze_basic_metrics) (class in cell_abm_pipeline.flows.analyze_cell_shapes) (class in cell_abm_pipeline.flows.analyze_colony_dynamics) (class in cell_abm_pipeline.flows.calculate_coefficients) (class in cell_abm_pipeline.flows.calculate_image_properties) (class in cell_abm_pipeline.flows.calculate_neighbors) (class in cell_abm_pipeline.flows.calculate_positions) (class in cell_abm_pipeline.flows.calculate_properties) (class in cell_abm_pipeline.flows.convert_arcade_format) (class in cell_abm_pipeline.flows.convert_physicell_format) (class in cell_abm_pipeline.flows.download_images) (class in cell_abm_pipeline.flows.generate_voronoi_tessellation) (class in cell_abm_pipeline.flows.group_basic_metrics) (class in cell_abm_pipeline.flows.group_cell_shapes) (class in cell_abm_pipeline.flows.group_colony_dynamics) (class in cell_abm_pipeline.flows.group_resource_usage) (class in cell_abm_pipeline.flows.initialize_arcade_simulations) (class in cell_abm_pipeline.flows.initialize_physicell_simulations) (class in cell_abm_pipeline.flows.make_simulation_movies) (class in cell_abm_pipeline.flows.organize_calculation_files) (class in cell_abm_pipeline.flows.parse_arcade_simulations) (class in cell_abm_pipeline.flows.parse_physicell_simulations) (class in cell_abm_pipeline.flows.plot_basic_metrics) (class in cell_abm_pipeline.flows.plot_cell_shapes) (class in cell_abm_pipeline.flows.plot_colony_dynamics) (class in cell_abm_pipeline.flows.plot_resource_usage) (class in cell_abm_pipeline.flows.process_sample) (class in cell_abm_pipeline.flows.run_batch_simulations) (class in cell_abm_pipeline.flows.run_docker_simulations) (class in cell_abm_pipeline.flows.run_fargate_calculations) (class in cell_abm_pipeline.flows.sample_image) (class in cell_abm_pipeline.flows.summarize_manifest) convert_to_arcade (ParametersConfig attribute) coordinate_type (ParametersConfig attribute) counts (ParametersConfig attribute) critical_heights (ParametersConfigConvertToArcade attribute) critical_volumes (ParametersConfigConvertToArcade attribute) D delta (ParametersConfigShapeModes attribute) ds (ParametersConfig attribute), [1], [2], [3] (ParametersConfigColonyContours attribute) (ParametersConfigColorizer attribute) (ParametersConfigProjections attribute) (ParametersConfigShapeContours attribute) (ParametersConfigSimulariumObjects attribute) (ParametersConfigSimulariumShapes attribute) dt (ParametersConfig attribute), [1], [2] (ParametersConfigCentroids attribute) (ParametersConfigColonyContours attribute) (ParametersConfigColorizer attribute) (ParametersConfigProjections attribute) (ParametersConfigShapeContours attribute) (ParametersConfigSimulariumObjects attribute) (ParametersConfigSimulariumShapes attribute) E edge_padding (ParametersConfig attribute) edge_threshold (ParametersConfig attribute) exceptions (ParametersConfigWallClock attribute) exclude_filters (ParametersConfig attribute), [1], [2] exclude_ids (ParametersConfig attribute) extension (ParametersConfig attribute) extensions (SeriesConfig attribute), [1], [2], [3] F feature_components (ParametersConfig attribute) feature_correlations (ParametersConfig attribute), [1] feature_distributions (ParametersConfig attribute), [1], [2], [3] feature_temporal (ParametersConfig attribute), [1] features (ParametersConfig attribute) (ParametersConfigColorizer attribute) (ParametersConfigFeatureComponents attribute) (ParametersConfigFeatureDistributions attribute), [1] (ParametersConfigFeatureTemporal attribute), [1] (ParametersConfigNeighborPositions attribute), [1] formats (ParametersConfig attribute), [1], [2] frame_spec (ParametersConfig attribute) (ParametersConfigCentroids attribute) (ParametersConfigColorizer attribute) (ParametersConfigImages attribute) (ParametersConfigMeshes attribute) (ParametersConfigProjections attribute) (ParametersConfigScan attribute) (ParametersConfigSimulariumObjects attribute) (ParametersConfigSimulariumShapes attribute) G get_docker_arguments() (in module cell_abm_pipeline.flows.initialize_arcade_simulations) grid (ParametersConfig attribute), [1] group_size (ParametersConfigSimulariumObjects attribute) groups (ParametersConfig attribute), [1], [2], [3] (SeriesConfig attribute), [1] H heights (ParametersConfigConvertToArcade attribute) I image (ParametersConfig attribute), [1], [2], [3] IMAGE_PROPERTIES (Calculation attribute) images (ParametersConfig attribute) include_bins (ParametersConfigFeatureCorrelations attribute) include_filters (ParametersConfig attribute), [1], [2] include_ids (ParametersConfig attribute) index_spec (ParametersConfigScan attribute) indices (ParametersConfigShapeSamples attribute) inits (SeriesConfig attribute), [1] invert (ParametersConfigMeshes attribute) iterations (ParametersConfig attribute) K key (ParametersConfig attribute), [1], [2], [3], [4], [5], [6] L limits (ParametersConfigFeatureCorrelations attribute) log_filter (ParametersConfig attribute), [1] M make_bar_figure() (in module cell_abm_pipeline.tasks.make_bar_figure) make_box_figure() (in module cell_abm_pipeline.tasks.make_box_figure) make_centroids_figure() (in module cell_abm_pipeline.tasks.make_centroids_figure) make_contour_figure() (in module cell_abm_pipeline.tasks.make_contour_figure) make_density_figure() (in module cell_abm_pipeline.tasks.make_density_figure) make_graph_figure() (in module cell_abm_pipeline.tasks.make_graph_figure) make_heatmap_figure() (in module cell_abm_pipeline.tasks.make_heatmap_figure) make_histogram_figure() (in module cell_abm_pipeline.tasks.make_histogram_figure) make_line_figure() (in module cell_abm_pipeline.tasks.make_line_figure) make_range_figure() (in module cell_abm_pipeline.tasks.make_range_figure) make_scatter_figure() (in module cell_abm_pipeline.tasks.make_scatter_figure) manifest_key (SeriesConfig attribute), [1], [2], [3], [4] manifest_location (ContextConfig attribute), [1], [2], [3], [4] margins (ParametersConfigConvertToArcade attribute) memory (ContextConfig attribute), [1] meshes (ParametersConfig attribute) metadata_key (SeriesConfig attribute) metadata_location (ContextConfig attribute) metrics (ParametersConfigMetricsBins attribute), [1] (ParametersConfigMetricsDistributions attribute), [1] (ParametersConfigMetricsIndividuals attribute), [1] (ParametersConfigMetricsSpatial attribute), [1] (ParametersConfigMetricsTemporal attribute), [1] metrics_bins (ParametersConfig attribute), [1] metrics_distributions (ParametersConfig attribute), [1] metrics_individuals (ParametersConfig attribute), [1] metrics_spatial (ParametersConfig attribute), [1] metrics_temporal (ParametersConfig attribute), [1] mode_correlations (ParametersConfig attribute), [1] model (ParametersConfig attribute), [1] module cell_abm_pipeline.flows cell_abm_pipeline.flows.analyze_basic_metrics cell_abm_pipeline.flows.analyze_cell_shapes cell_abm_pipeline.flows.analyze_colony_dynamics cell_abm_pipeline.flows.calculate_coefficients cell_abm_pipeline.flows.calculate_image_properties cell_abm_pipeline.flows.calculate_neighbors cell_abm_pipeline.flows.calculate_positions cell_abm_pipeline.flows.calculate_properties cell_abm_pipeline.flows.convert_arcade_format cell_abm_pipeline.flows.convert_physicell_format cell_abm_pipeline.flows.demo cell_abm_pipeline.flows.download_images cell_abm_pipeline.flows.generate_voronoi_tessellation cell_abm_pipeline.flows.group_basic_metrics cell_abm_pipeline.flows.group_cell_shapes cell_abm_pipeline.flows.group_colony_dynamics cell_abm_pipeline.flows.group_resource_usage cell_abm_pipeline.flows.initialize_arcade_simulations cell_abm_pipeline.flows.initialize_physicell_simulations cell_abm_pipeline.flows.make_simulation_movies cell_abm_pipeline.flows.organize_calculation_files cell_abm_pipeline.flows.parse_arcade_simulations cell_abm_pipeline.flows.parse_physicell_simulations cell_abm_pipeline.flows.plot_basic_metrics cell_abm_pipeline.flows.plot_cell_shapes cell_abm_pipeline.flows.plot_colony_dynamics cell_abm_pipeline.flows.plot_resource_usage cell_abm_pipeline.flows.process_sample cell_abm_pipeline.flows.run_batch_simulations cell_abm_pipeline.flows.run_docker_simulations cell_abm_pipeline.flows.run_fargate_calculations cell_abm_pipeline.flows.sample_image cell_abm_pipeline.flows.summarize_manifest cell_abm_pipeline.tasks cell_abm_pipeline.tasks.bin_to_hex cell_abm_pipeline.tasks.build_svg_image cell_abm_pipeline.tasks.calculate_category_durations cell_abm_pipeline.tasks.calculate_data_bins cell_abm_pipeline.tasks.check_data_bounds cell_abm_pipeline.tasks.make_bar_figure cell_abm_pipeline.tasks.make_box_figure cell_abm_pipeline.tasks.make_centroids_figure cell_abm_pipeline.tasks.make_contour_figure cell_abm_pipeline.tasks.make_density_figure cell_abm_pipeline.tasks.make_graph_figure cell_abm_pipeline.tasks.make_heatmap_figure cell_abm_pipeline.tasks.make_histogram_figure cell_abm_pipeline.tasks.make_line_figure cell_abm_pipeline.tasks.make_range_figure cell_abm_pipeline.tasks.make_scatter_figure cell_abm_pipeline.tasks.physicell N name (SeriesConfig attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31] neighbor_positions (ParametersConfig attribute), [1] NEIGHBORS (Calculation attribute) O object_storage (ParametersConfig attribute), [1] offset (ParametersConfig attribute), [1] order (ParametersConfig attribute) (ParametersConfigShapeAverage attribute) (ParametersConfigShapeModes attribute) outlier (ParametersConfig attribute) overrides (ParametersConfig attribute) P ParametersConfig (class in cell_abm_pipeline.flows.analyze_basic_metrics) (class in cell_abm_pipeline.flows.analyze_cell_shapes) (class in cell_abm_pipeline.flows.analyze_colony_dynamics) (class in cell_abm_pipeline.flows.calculate_coefficients) (class in cell_abm_pipeline.flows.calculate_image_properties) (class in cell_abm_pipeline.flows.calculate_neighbors) (class in cell_abm_pipeline.flows.calculate_positions) (class in cell_abm_pipeline.flows.calculate_properties) (class in cell_abm_pipeline.flows.convert_arcade_format) (class in cell_abm_pipeline.flows.convert_physicell_format) (class in cell_abm_pipeline.flows.download_images) (class in cell_abm_pipeline.flows.generate_voronoi_tessellation) (class in cell_abm_pipeline.flows.group_basic_metrics) (class in cell_abm_pipeline.flows.group_cell_shapes) (class in cell_abm_pipeline.flows.group_colony_dynamics) (class in cell_abm_pipeline.flows.group_resource_usage) (class in cell_abm_pipeline.flows.initialize_arcade_simulations) (class in cell_abm_pipeline.flows.initialize_physicell_simulations) (class in cell_abm_pipeline.flows.make_simulation_movies) (class in cell_abm_pipeline.flows.organize_calculation_files) (class in cell_abm_pipeline.flows.parse_arcade_simulations) (class in cell_abm_pipeline.flows.parse_physicell_simulations) (class in cell_abm_pipeline.flows.plot_basic_metrics) (class in cell_abm_pipeline.flows.plot_cell_shapes) (class in cell_abm_pipeline.flows.plot_colony_dynamics) (class in cell_abm_pipeline.flows.plot_resource_usage) (class in cell_abm_pipeline.flows.process_sample) (class in cell_abm_pipeline.flows.run_batch_simulations) (class in cell_abm_pipeline.flows.run_docker_simulations) (class in cell_abm_pipeline.flows.run_fargate_calculations) (class in cell_abm_pipeline.flows.sample_image) (class in cell_abm_pipeline.flows.summarize_manifest) ParametersConfigCentroids (class in cell_abm_pipeline.flows.make_simulation_movies) ParametersConfigColonyContours (class in cell_abm_pipeline.flows.group_colony_dynamics) ParametersConfigColorizer (class in cell_abm_pipeline.flows.convert_arcade_format) ParametersConfigConvertToArcade (class in cell_abm_pipeline.flows.initialize_arcade_simulations) ParametersConfigFeatureComponents (class in cell_abm_pipeline.flows.group_cell_shapes) ParametersConfigFeatureCorrelations (class in cell_abm_pipeline.flows.group_cell_shapes) (class in cell_abm_pipeline.flows.plot_cell_shapes) ParametersConfigFeatureDistributions (class in cell_abm_pipeline.flows.group_cell_shapes) (class in cell_abm_pipeline.flows.group_colony_dynamics) (class in cell_abm_pipeline.flows.plot_cell_shapes) (class in cell_abm_pipeline.flows.plot_colony_dynamics) ParametersConfigFeatureTemporal (class in cell_abm_pipeline.flows.group_colony_dynamics) (class in cell_abm_pipeline.flows.plot_colony_dynamics) ParametersConfigImages (class in cell_abm_pipeline.flows.convert_arcade_format) ParametersConfigMeshes (class in cell_abm_pipeline.flows.convert_arcade_format) ParametersConfigMetricsBins (class in cell_abm_pipeline.flows.group_basic_metrics) (class in cell_abm_pipeline.flows.plot_basic_metrics) ParametersConfigMetricsDistributions (class in cell_abm_pipeline.flows.group_basic_metrics) (class in cell_abm_pipeline.flows.plot_basic_metrics) ParametersConfigMetricsIndividuals (class in cell_abm_pipeline.flows.group_basic_metrics) (class in cell_abm_pipeline.flows.plot_basic_metrics) ParametersConfigMetricsSpatial (class in cell_abm_pipeline.flows.group_basic_metrics) (class in cell_abm_pipeline.flows.plot_basic_metrics) ParametersConfigMetricsTemporal (class in cell_abm_pipeline.flows.group_basic_metrics) (class in cell_abm_pipeline.flows.plot_basic_metrics) ParametersConfigModeCorrelations (class in cell_abm_pipeline.flows.group_cell_shapes) (class in cell_abm_pipeline.flows.plot_cell_shapes) ParametersConfigNeighborPositions (class in cell_abm_pipeline.flows.group_colony_dynamics) (class in cell_abm_pipeline.flows.plot_colony_dynamics) ParametersConfigObjectStorage (class in cell_abm_pipeline.flows.group_resource_usage) (class in cell_abm_pipeline.flows.plot_resource_usage) ParametersConfigPopulationCounts (class in cell_abm_pipeline.flows.group_basic_metrics) (class in cell_abm_pipeline.flows.group_cell_shapes) (class in cell_abm_pipeline.flows.plot_basic_metrics) (class in cell_abm_pipeline.flows.plot_cell_shapes) ParametersConfigPopulationStats (class in cell_abm_pipeline.flows.group_cell_shapes) (class in cell_abm_pipeline.flows.plot_cell_shapes) ParametersConfigProjections (class in cell_abm_pipeline.flows.convert_arcade_format) ParametersConfigScan (class in cell_abm_pipeline.flows.make_simulation_movies) ParametersConfigShapeAverage (class in cell_abm_pipeline.flows.group_cell_shapes) (class in cell_abm_pipeline.flows.plot_cell_shapes) ParametersConfigShapeContours (class in cell_abm_pipeline.flows.group_cell_shapes) ParametersConfigShapeErrors (class in cell_abm_pipeline.flows.group_cell_shapes) (class in cell_abm_pipeline.flows.plot_cell_shapes) ParametersConfigShapeModes (class in cell_abm_pipeline.flows.group_cell_shapes) (class in cell_abm_pipeline.flows.plot_cell_shapes) ParametersConfigShapeSamples (class in cell_abm_pipeline.flows.group_cell_shapes) ParametersConfigSimulariumObjects (class in cell_abm_pipeline.flows.convert_arcade_format) ParametersConfigSimulariumShapes (class in cell_abm_pipeline.flows.convert_arcade_format) ParametersConfigVarianceExplained (class in cell_abm_pipeline.flows.group_cell_shapes) (class in cell_abm_pipeline.flows.plot_cell_shapes) ParametersConfigWallClock (class in cell_abm_pipeline.flows.group_resource_usage) (class in cell_abm_pipeline.flows.plot_resource_usage) pattern (ParametersConfigObjectStorage attribute) (ParametersConfigWallClock attribute) phase_colors (ParametersConfigMetricsIndividuals attribute) (ParametersConfigMetricsSpatial attribute) (ParametersConfigSimulariumObjects attribute) (ParametersConfigSimulariumShapes attribute) phases (ParametersConfigMetricsDistributions attribute), [1] (ParametersConfigMetricsTemporal attribute), [1] plots (ParametersConfig attribute), [1], [2], [3] point (ParametersConfigShapeModes attribute) population_colors (ParametersConfigMetricsSpatial attribute) population_counts (ParametersConfig attribute), [1], [2], [3] population_stats (ParametersConfig attribute), [1] populations (ParametersConfigMetricsTemporal attribute), [1] POSITIONS (Calculation attribute) potts_terms (ParametersConfigConvertToArcade attribute) process_samples (ParametersConfig attribute) projection (ParametersConfigColonyContours attribute) (ParametersConfigShapeContours attribute) projections (ParametersConfig attribute) (ParametersConfigShapeAverage attribute), [1] (ParametersConfigShapeModes attribute), [1] PROPERTIES (Calculation attribute) properties (ParametersConfig attribute), [1] (ParametersConfigFeatureCorrelations attribute), [1] (ParametersConfigFeatureDistributions attribute), [1] Q queue (ContextConfig attribute) quilt_package (ParametersConfig attribute) quilt_registry (ParametersConfig attribute) R reference (ParametersConfig attribute) reference_coefficients (ParametersConfigFeatureDistributions attribute) reference_data (ParametersConfigModeCorrelations attribute) reference_key (SeriesConfig attribute) reference_location (ContextConfig attribute) reference_metrics (ParametersConfigFeatureComponents attribute) (ParametersConfigFeatureDistributions attribute) reference_model (ParametersConfigFeatureDistributions attribute) (ParametersConfigModeCorrelations attribute) reference_properties (ParametersConfigFeatureComponents attribute) (ParametersConfigFeatureDistributions attribute) region (ContextConfig attribute), [1] (ParametersConfig attribute), [1], [2], [3] region_colors (ParametersConfigProjections attribute) (ParametersConfigScan attribute) regions (ParametersConfig attribute), [1], [2] (ParametersConfigColonyContours attribute) (ParametersConfigColorizer attribute) (ParametersConfigConvertToArcade attribute) (ParametersConfigFeatureComponents attribute) (ParametersConfigFeatureCorrelations attribute), [1] (ParametersConfigFeatureDistributions attribute), [1] (ParametersConfigImages attribute) (ParametersConfigMeshes attribute) (ParametersConfigMetricsDistributions attribute), [1] (ParametersConfigMetricsIndividuals attribute), [1] (ParametersConfigMetricsSpatial attribute), [1] (ParametersConfigMetricsTemporal attribute), [1] (ParametersConfigModeCorrelations attribute) (ParametersConfigPopulationCounts attribute) (ParametersConfigPopulationStats attribute) (ParametersConfigProjections attribute) (ParametersConfigScan attribute) (ParametersConfigShapeAverage attribute) (ParametersConfigShapeContours attribute) (ParametersConfigShapeErrors attribute) (ParametersConfigShapeModes attribute), [1] (ParametersConfigShapeSamples attribute) (ParametersConfigVarianceExplained attribute) remove_edges (ParametersConfig attribute) remove_unconnected (ParametersConfig attribute) resolution (ParametersConfig attribute), [1] (ParametersConfigSimulariumShapes attribute) retries (ParametersConfig attribute), [1] retry_delay (ParametersConfig attribute), [1] run_flow() (in module cell_abm_pipeline.flows.analyze_basic_metrics) (in module cell_abm_pipeline.flows.analyze_cell_shapes) (in module cell_abm_pipeline.flows.analyze_colony_dynamics) (in module cell_abm_pipeline.flows.calculate_coefficients) (in module cell_abm_pipeline.flows.calculate_image_properties) (in module cell_abm_pipeline.flows.calculate_neighbors) (in module cell_abm_pipeline.flows.calculate_positions) (in module cell_abm_pipeline.flows.calculate_properties) (in module cell_abm_pipeline.flows.convert_arcade_format) (in module cell_abm_pipeline.flows.convert_physicell_format) (in module cell_abm_pipeline.flows.demo) (in module cell_abm_pipeline.flows.download_images) (in module cell_abm_pipeline.flows.generate_voronoi_tessellation) (in module cell_abm_pipeline.flows.group_basic_metrics) (in module cell_abm_pipeline.flows.group_cell_shapes) (in module cell_abm_pipeline.flows.group_colony_dynamics) (in module cell_abm_pipeline.flows.group_resource_usage) (in module cell_abm_pipeline.flows.initialize_arcade_simulations) (in module cell_abm_pipeline.flows.initialize_physicell_simulations) (in module cell_abm_pipeline.flows.make_simulation_movies) (in module cell_abm_pipeline.flows.organize_calculation_files) (in module cell_abm_pipeline.flows.parse_arcade_simulations) (in module cell_abm_pipeline.flows.parse_physicell_simulations) (in module cell_abm_pipeline.flows.plot_basic_metrics) (in module cell_abm_pipeline.flows.plot_cell_shapes) (in module cell_abm_pipeline.flows.plot_colony_dynamics) (in module cell_abm_pipeline.flows.plot_resource_usage) (in module cell_abm_pipeline.flows.process_sample) (in module cell_abm_pipeline.flows.run_batch_simulations) (in module cell_abm_pipeline.flows.run_docker_simulations) (in module cell_abm_pipeline.flows.run_fargate_calculations) (in module cell_abm_pipeline.flows.sample_image) (in module cell_abm_pipeline.flows.summarize_manifest) run_flow_analyze_measures() (in module cell_abm_pipeline.flows.analyze_colony_dynamics) run_flow_analyze_stats() (in module cell_abm_pipeline.flows.analyze_cell_shapes) run_flow_combine_data() (in module cell_abm_pipeline.flows.analyze_cell_shapes) run_flow_compress_files() (in module cell_abm_pipeline.flows.organize_calculation_files) run_flow_convert_to_arcade() (in module cell_abm_pipeline.flows.initialize_arcade_simulations) run_flow_convert_to_colorizer() (in module cell_abm_pipeline.flows.convert_arcade_format) run_flow_convert_to_images() (in module cell_abm_pipeline.flows.convert_arcade_format) run_flow_convert_to_meshes() (in module cell_abm_pipeline.flows.convert_arcade_format) run_flow_convert_to_projections() (in module cell_abm_pipeline.flows.convert_arcade_format) run_flow_convert_to_simularium() (in module cell_abm_pipeline.flows.convert_physicell_format) run_flow_convert_to_simularium_objects() (in module cell_abm_pipeline.flows.convert_arcade_format) run_flow_convert_to_simularium_shapes() (in module cell_abm_pipeline.flows.convert_arcade_format) run_flow_fit_models() (in module cell_abm_pipeline.flows.analyze_cell_shapes) run_flow_generate_networks() (in module cell_abm_pipeline.flows.analyze_colony_dynamics) run_flow_group_colony_contours() (in module cell_abm_pipeline.flows.group_colony_dynamics) run_flow_group_feature_components() (in module cell_abm_pipeline.flows.group_cell_shapes) run_flow_group_feature_correlations() (in module cell_abm_pipeline.flows.group_cell_shapes) run_flow_group_feature_distributions() (in module cell_abm_pipeline.flows.group_cell_shapes) (in module cell_abm_pipeline.flows.group_colony_dynamics) run_flow_group_feature_temporal() (in module cell_abm_pipeline.flows.group_colony_dynamics) run_flow_group_metrics_bins() (in module cell_abm_pipeline.flows.group_basic_metrics) run_flow_group_metrics_distributions() (in module cell_abm_pipeline.flows.group_basic_metrics) run_flow_group_metrics_individuals() (in module cell_abm_pipeline.flows.group_basic_metrics) run_flow_group_metrics_spatial() (in module cell_abm_pipeline.flows.group_basic_metrics) run_flow_group_metrics_temporal() (in module cell_abm_pipeline.flows.group_basic_metrics) run_flow_group_mode_correlations() (in module cell_abm_pipeline.flows.group_cell_shapes) run_flow_group_neighbor_positions() (in module cell_abm_pipeline.flows.group_colony_dynamics) run_flow_group_object_storage() (in module cell_abm_pipeline.flows.group_resource_usage) run_flow_group_population_counts() (in module cell_abm_pipeline.flows.group_basic_metrics) (in module cell_abm_pipeline.flows.group_cell_shapes) run_flow_group_population_stats() (in module cell_abm_pipeline.flows.group_cell_shapes) run_flow_group_shape_average() (in module cell_abm_pipeline.flows.group_cell_shapes) run_flow_group_shape_contours() (in module cell_abm_pipeline.flows.group_cell_shapes) run_flow_group_shape_errors() (in module cell_abm_pipeline.flows.group_cell_shapes) run_flow_group_shape_modes() (in module cell_abm_pipeline.flows.group_cell_shapes) run_flow_group_shape_samples() (in module cell_abm_pipeline.flows.group_cell_shapes) run_flow_group_variance_explained() (in module cell_abm_pipeline.flows.group_cell_shapes) run_flow_group_wall_clock() (in module cell_abm_pipeline.flows.group_resource_usage) run_flow_make_centroids_movie() (in module cell_abm_pipeline.flows.make_simulation_movies) run_flow_make_scan_movie() (in module cell_abm_pipeline.flows.make_simulation_movies) run_flow_merge_files() (in module cell_abm_pipeline.flows.organize_calculation_files) run_flow_plot_feature_correlations() (in module cell_abm_pipeline.flows.plot_cell_shapes) run_flow_plot_feature_distributions() (in module cell_abm_pipeline.flows.plot_cell_shapes) (in module cell_abm_pipeline.flows.plot_colony_dynamics) run_flow_plot_feature_temporal() (in module cell_abm_pipeline.flows.plot_colony_dynamics) run_flow_plot_metrics_bins() (in module cell_abm_pipeline.flows.plot_basic_metrics) run_flow_plot_metrics_distributions() (in module cell_abm_pipeline.flows.plot_basic_metrics) run_flow_plot_metrics_individuals() (in module cell_abm_pipeline.flows.plot_basic_metrics) run_flow_plot_metrics_spatial() (in module cell_abm_pipeline.flows.plot_basic_metrics) run_flow_plot_metrics_temporal() (in module cell_abm_pipeline.flows.plot_basic_metrics) run_flow_plot_mode_correlations() (in module cell_abm_pipeline.flows.plot_cell_shapes) run_flow_plot_neighbor_positions() (in module cell_abm_pipeline.flows.plot_colony_dynamics) run_flow_plot_object_storage() (in module cell_abm_pipeline.flows.plot_resource_usage) run_flow_plot_population_counts() (in module cell_abm_pipeline.flows.plot_basic_metrics) (in module cell_abm_pipeline.flows.plot_cell_shapes) run_flow_plot_population_stats() (in module cell_abm_pipeline.flows.plot_cell_shapes) run_flow_plot_shape_average() (in module cell_abm_pipeline.flows.plot_cell_shapes) run_flow_plot_shape_errors() (in module cell_abm_pipeline.flows.plot_cell_shapes) run_flow_plot_shape_modes() (in module cell_abm_pipeline.flows.plot_cell_shapes) run_flow_plot_variance_explained() (in module cell_abm_pipeline.flows.plot_cell_shapes) run_flow_plot_wall_clock() (in module cell_abm_pipeline.flows.plot_resource_usage) run_flow_process_coefficients() (in module cell_abm_pipeline.flows.analyze_cell_shapes) run_flow_process_data() (in module cell_abm_pipeline.flows.analyze_colony_dynamics) run_flow_process_properties() (in module cell_abm_pipeline.flows.analyze_cell_shapes) run_flow_process_results() (in module cell_abm_pipeline.flows.analyze_basic_metrics) run_flow_process_samples() (in module cell_abm_pipeline.flows.initialize_arcade_simulations) run_flow_remove_files() (in module cell_abm_pipeline.flows.organize_calculation_files) run_flow_sample_images() (in module cell_abm_pipeline.flows.initialize_arcade_simulations) S sample_images (ParametersConfig attribute) sample_replicates (ParametersConfig attribute) sample_size (ParametersConfig attribute) save_logs (ParametersConfig attribute), [1] scale (ParametersConfig attribute) (ParametersConfigMetricsBins attribute), [1] (ParametersConfigProjections attribute) (ParametersConfigShapeAverage attribute), [1] (ParametersConfigShapeModes attribute) scale_xy (ParametersConfig attribute) scale_z (ParametersConfig attribute) scan (ParametersConfig attribute) search_locations (ParametersConfig attribute) (ParametersConfigObjectStorage attribute) (ParametersConfigWallClock attribute) secret_access_key (ContextConfig attribute) security_groups (ContextConfig attribute) seed (ParametersConfig attribute), [1], [2], [3], [4] (ParametersConfigColonyContours attribute) (ParametersConfigMetricsBins attribute) (ParametersConfigMetricsIndividuals attribute), [1] (ParametersConfigNeighborPositions attribute), [1] (ParametersConfigShapeContours attribute) (ParametersConfigShapeSamples attribute) seeds (ParametersConfigCentroids attribute) (ParametersConfigColorizer attribute) (ParametersConfigImages attribute) (ParametersConfigMeshes attribute) (ParametersConfigMetricsBins attribute) (ParametersConfigMetricsDistributions attribute) (ParametersConfigMetricsSpatial attribute), [1] (ParametersConfigMetricsTemporal attribute) (ParametersConfigPopulationCounts attribute), [1] (ParametersConfigProjections attribute) (ParametersConfigScan attribute) (ParametersConfigSimulariumObjects attribute) (ParametersConfigSimulariumShapes attribute) (SeriesConfig attribute), [1], [2], [3], [4], [5], [6], [7], [8] seeds_per_job (ParametersConfig attribute), [1] separate (ParametersConfigImages attribute) SeriesConfig (class in cell_abm_pipeline.flows.analyze_basic_metrics) (class in cell_abm_pipeline.flows.analyze_cell_shapes) (class in cell_abm_pipeline.flows.analyze_colony_dynamics) (class in cell_abm_pipeline.flows.calculate_coefficients) (class in cell_abm_pipeline.flows.calculate_image_properties) (class in cell_abm_pipeline.flows.calculate_neighbors) (class in cell_abm_pipeline.flows.calculate_positions) (class in cell_abm_pipeline.flows.calculate_properties) (class in cell_abm_pipeline.flows.convert_arcade_format) (class in cell_abm_pipeline.flows.convert_physicell_format) (class in cell_abm_pipeline.flows.download_images) (class in cell_abm_pipeline.flows.generate_voronoi_tessellation) (class in cell_abm_pipeline.flows.group_basic_metrics) (class in cell_abm_pipeline.flows.group_cell_shapes) (class in cell_abm_pipeline.flows.group_colony_dynamics) (class in cell_abm_pipeline.flows.group_resource_usage) (class in cell_abm_pipeline.flows.initialize_arcade_simulations) (class in cell_abm_pipeline.flows.initialize_physicell_simulations) (class in cell_abm_pipeline.flows.make_simulation_movies) (class in cell_abm_pipeline.flows.organize_calculation_files) (class in cell_abm_pipeline.flows.parse_arcade_simulations) (class in cell_abm_pipeline.flows.parse_physicell_simulations) (class in cell_abm_pipeline.flows.plot_basic_metrics) (class in cell_abm_pipeline.flows.plot_cell_shapes) (class in cell_abm_pipeline.flows.plot_colony_dynamics) (class in cell_abm_pipeline.flows.plot_resource_usage) (class in cell_abm_pipeline.flows.process_sample) (class in cell_abm_pipeline.flows.run_batch_simulations) (class in cell_abm_pipeline.flows.run_docker_simulations) (class in cell_abm_pipeline.flows.run_fargate_calculations) (class in cell_abm_pipeline.flows.sample_image) (class in cell_abm_pipeline.flows.summarize_manifest) shape_average (ParametersConfig attribute), [1] shape_contours (ParametersConfig attribute) shape_errors (ParametersConfig attribute), [1] shape_modes (ParametersConfig attribute), [1] shape_samples (ParametersConfig attribute) simularium_objects (ParametersConfig attribute) simularium_shapes (ParametersConfig attribute) slice_index (ParametersConfigColonyContours attribute) (ParametersConfigShapeContours attribute) state_thresholds (ParametersConfigConvertToArcade attribute) submit_tasks (ParametersConfig attribute) subnets (ContextConfig attribute) substrate (ParametersConfig attribute) substrate_color (ParametersConfig attribute) suffix (ParametersConfig attribute) T target_height (ParametersConfig attribute) template_key (SeriesConfig attribute), [1] template_location (ContextConfig attribute), [1] terminate_jobs (ParametersConfig attribute), [1] threshold (ParametersConfigMetricsDistributions attribute) tick (ParametersConfig attribute), [1], [2], [3], [4] (ParametersConfigPopulationCounts attribute), [1] (ParametersConfigShapeSamples attribute) ticks (ParametersConfig attribute), [1] (ParametersConfigMetricsBins attribute) (ParametersConfigMetricsSpatial attribute) (ParametersConfigNeighborPositions attribute), [1] time (ParametersConfigColonyContours attribute) (ParametersConfigMetricsBins attribute) (ParametersConfigPopulationCounts attribute), [1] (ParametersConfigShapeContours attribute) times (ParametersConfigMetricsSpatial attribute) timestep (ParametersConfig attribute) U unconnected_filter (ParametersConfig attribute) unconnected_threshold (ParametersConfig attribute) update_manifest (ParametersConfig attribute) url (ParametersConfigSimulariumObjects attribute) user (ContextConfig attribute), [1] V valid_phases (ParametersConfig attribute) valid_ticks (ParametersConfig attribute) valid_times (ParametersConfig attribute) variance_explained (ParametersConfig attribute), [1] vcpus (ContextConfig attribute), [1] view (ParametersConfigScan attribute) volumes (ParametersConfigConvertToArcade attribute) W wall_clock (ParametersConfig attribute), [1] window (ParametersConfigCentroids attribute) working_location (ContextConfig attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31] X x_bounds (ParametersConfigCentroids attribute) (ParametersConfigScan attribute) Y y_bounds (ParametersConfigCentroids attribute) (ParametersConfigScan attribute)