Index Symbols | _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | Z Symbols --dataset command line option --excel_path command line option --extractor command line option --extractors command line option --gpu command line option, [1] --graph_methods command line option --model command line option --output_path command line option, [1] --patch_overlap command line option --patch_size command line option --patched_slide_path command line option, [1] --segmentation_model command line option --segmentation_models command line option --target_mag command line option --wsi_path command line option, [1], [2] _ __call__() (cellmil.utils.train.losses.NegativeLogLikelihoodSurvLoss method) __getitem__() (cellmil.datamodels.datasets.cell_mil_dataset.CellMILDataset method) (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) (cellmil.datamodels.datasets.neoplastic_dataset.NeoplasticDataset method) (cellmil.datamodels.datasets.NeoplasticDataset method) (cellmil.datamodels.datasets.patch_mil_dataset.PatchMILDataset method) (cellmil.datamodels.transforms.label_pipeline.LabelTransformPipeline method) (cellmil.datamodels.transforms.LabelTransformPipeline method) (cellmil.datamodels.transforms.pipeline.TransformPipeline method) (cellmil.datamodels.transforms.TransformPipeline method) __init__() (cellmil.data.cucim_deepzoom.DeepZoomGeneratorCucim method) (cellmil.data.patch_extractor.PatchExtractor method) (cellmil.data.PatchExtractor method) (cellmil.data.storage.Storage method) (cellmil.datamodels.datasets.cell_gnn_mil_dataset.CellGNNMILDataset method) (cellmil.datamodels.datasets.cell_gnn_mil_dataset.SubsetCellGNNMILDataset method) (cellmil.datamodels.datasets.cell_mil_dataset.CellMILDataset method) (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) (cellmil.datamodels.datasets.neoplastic_dataset.NeoplasticDataset method) (cellmil.datamodels.datasets.NeoplasticDataset method) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset method) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.SubsetPatchGNNMILDataset method) (cellmil.datamodels.datasets.patch_mil_dataset.PatchMILDataset method) (cellmil.datamodels.model.ExperimentMetadata method) (cellmil.datamodels.model.FoldMetadata method) (cellmil.datamodels.model.ModelStorage method) (cellmil.datamodels.transforms.base_label_transform.FittableLabelTransform method) (cellmil.datamodels.transforms.base_label_transform.LabelTransform method) (cellmil.datamodels.transforms.base_transform.FittableTransform method) (cellmil.datamodels.transforms.base_transform.Transform method) (cellmil.datamodels.transforms.correlation_filter.CorrelationFilterTransform method) (cellmil.datamodels.transforms.CorrelationFilterTransform method) (cellmil.datamodels.transforms.FittableLabelTransform method) (cellmil.datamodels.transforms.FittableTransform method) (cellmil.datamodels.transforms.label_pipeline.LabelTransformPipeline method) (cellmil.datamodels.transforms.LabelTransform method) (cellmil.datamodels.transforms.LabelTransformPipeline method) (cellmil.datamodels.transforms.normalization.RobustScalerTransform method) (cellmil.datamodels.transforms.pipeline.TransformPipeline method) (cellmil.datamodels.transforms.RobustScalerTransform method) (cellmil.datamodels.transforms.time_discretizer.TimeDiscretizerTransform method) (cellmil.datamodels.transforms.TimeDiscretizerTransform method) (cellmil.datamodels.transforms.Transform method) (cellmil.datamodels.transforms.TransformPipeline method) (cellmil.datamodels.WSI method) (cellmil.datamodels.wsi.WSI method) (cellmil.dataset.dataset_creator.DatasetCreator method) (cellmil.dataset.DatasetCreator method) (cellmil.features.extractor.embedding.EmbeddingExtractor method) (cellmil.features.extractor.embedding.GigapathExtractor method) (cellmil.features.extractor.embedding.ResNet50Extractor method) (cellmil.features.extractor.embedding.UNIExtractor method) (cellmil.features.extractor.morphological.MorphologicalExtractor method) (cellmil.features.extractor.morphological.PyRadiomicsExtractor method) (cellmil.features.extractor.topological.ConnectivityExtractor method) (cellmil.features.extractor.topological.GeometricExtractor method) (cellmil.features.extractor.topological.StructureExtractor method) (cellmil.features.extractor.topological.TopologicalExtractor method) (cellmil.features.feature_extractor.FeatureExtractor method) (cellmil.features.FeatureExtractor method) (cellmil.graph.creator.Creator method) (cellmil.graph.creator.EdgeCreator method) (cellmil.graph.creator.SimilarityEdgeCreator method) (cellmil.graph.debug_visualizer.GraphDebugVisualizer method) (cellmil.graph.graph_creator.GraphCreator method) (cellmil.graph.GraphCreator method) (cellmil.interfaces.CellSegmenterConfig method) (cellmil.interfaces.DatasetCreatorConfig method) (cellmil.interfaces.FeatureExtractorConfig method) (cellmil.interfaces.FeatureVisualizerConfig method) (cellmil.interfaces.GraphCreatorConfig method) (cellmil.interfaces.MILPredictorConfig method) (cellmil.interfaces.MILTrainerConfig method) (cellmil.interfaces.PatchExtractorConfig method) (cellmil.interfaces.TableConfig.TableConfig method) (cellmil.models.mil.attentiondeepmil.AttentionDeepMIL method) (cellmil.models.mil.attentiondeepmil.LitAttentionDeepMIL method) (cellmil.models.mil.attentiondeepmil.LitSurvAttentionDeepMIL method) (cellmil.models.mil.cellconv.CellConv method) (cellmil.models.mil.cellconv.LitCellConv method) (cellmil.models.mil.cellconv.LitSurvCellConv method) (cellmil.models.mil.clam.Attn_Net method) (cellmil.models.mil.clam.Attn_Net_Gated method) (cellmil.models.mil.clam.CLAM_MB method) (cellmil.models.mil.clam.CLAM_SB method) (cellmil.models.mil.clam.CLAMTrainerLegacy method) (cellmil.models.mil.clam.LitCLAM method) (cellmil.models.mil.clam.LitSurvCLAM method) (cellmil.models.mil.graphmil.Attention method) (cellmil.models.mil.graphmil.CHIMERA method) (cellmil.models.mil.graphmil.CLAM method) (cellmil.models.mil.graphmil.EGNN method) (cellmil.models.mil.graphmil.GAT method) (cellmil.models.mil.graphmil.GATv2 method) (cellmil.models.mil.graphmil.GlobalPooling_Classifier method) (cellmil.models.mil.graphmil.GNN method) (cellmil.models.mil.graphmil.gnn.CHIMERA method) (cellmil.models.mil.graphmil.gnn.CHIMERA_block method) (cellmil.models.mil.graphmil.gnn.EGNN method) (cellmil.models.mil.graphmil.gnn.GAT method) (cellmil.models.mil.graphmil.gnn.GATv2 method) (cellmil.models.mil.graphmil.gnn.GNN method) (cellmil.models.mil.graphmil.gnn.SAGE method) (cellmil.models.mil.graphmil.gnn.SGFormer method) (cellmil.models.mil.graphmil.gnn.SGFormerAttention method) (cellmil.models.mil.graphmil.gnn.SmallWorld method) (cellmil.models.mil.graphmil.LitGraphMIL method) (cellmil.models.mil.graphmil.LitSurvGraphMIL method) (cellmil.models.mil.graphmil.Mean_MLP method) (cellmil.models.mil.graphmil.pool.Attention method) (cellmil.models.mil.graphmil.pool.CLAM method) (cellmil.models.mil.graphmil.pool.GlobalPooling_Classifier method) (cellmil.models.mil.graphmil.pool.Mean_MLP method) (cellmil.models.mil.graphmil.pool.Standard method) (cellmil.models.mil.graphmil.SAGE method) (cellmil.models.mil.graphmil.SGFormer method) (cellmil.models.mil.graphmil.SmallWorld method) (cellmil.models.mil.graphmil.Standard method) (cellmil.models.mil.head4type.Head4Type method) (cellmil.models.mil.head4type.LitHead4Type method) (cellmil.models.mil.head4type.LitSurvHead4Type method) (cellmil.models.mil.histobistro.Attention method) (cellmil.models.mil.histobistro.FeedForward method) (cellmil.models.mil.histobistro.HistoBistro method) (cellmil.models.mil.histobistro.PreNorm method) (cellmil.models.mil.histobistro.TransformerBlocks method) (cellmil.models.mil.LitAttentionDeepMIL method) (cellmil.models.mil.LitCLAM method) (cellmil.models.mil.LitGraphMIL method) (cellmil.models.mil.multifocus.LitMultiFocus method) (cellmil.models.mil.multifocus.MultiFocus method) (cellmil.models.mil.standard.MIL_fc method) (cellmil.models.mil.standard.MIL_fc_mc method) (cellmil.models.mil.transmil.PPEG method) (cellmil.models.mil.transmil.TransLayer method) (cellmil.models.mil.transmil.TransMIL method) (cellmil.models.mil.utils.Accuracy_Logger method) (cellmil.models.mil.utils.AEM method) (cellmil.models.mil.utils.EarlyStopping method) (cellmil.models.mil.utils.LitGeneral method) (cellmil.models.segmentation.cellpose.CellposeSAM method) (cellmil.models.segmentation.CellposeSAM method) (cellmil.models.segmentation.cellposeV2.CellposeSAM method) (cellmil.models.segmentation.cellvit.CellViT method) (cellmil.models.segmentation.cellvit.CellViTSAM method) (cellmil.models.segmentation.CellViTSAM method) (cellmil.models.segmentation.HoVerNet method) (cellmil.models.segmentation.hovernet._BatchNormRelu method) (cellmil.models.segmentation.hovernet._HoverNetDecoder method) (cellmil.models.segmentation.hovernet._HoVerNetDenseUnit method) (cellmil.models.segmentation.hovernet._HoVerNetEncoder method) (cellmil.models.segmentation.hovernet._HoVerNetResidualUnit method) (cellmil.models.segmentation.hovernet.HoVerNet method) (cellmil.segmentation.cell_segmenter.CellPostProcessor method) (cellmil.segmentation.cell_segmenter.CellSegmenter method) (cellmil.segmentation.CellSegmenter method) (cellmil.statistics.stats_printer.StatsPrinter method) (cellmil.statistics.StatsPrinter method) (cellmil.utils.stain_normalization.NormalizeParameters method) (cellmil.utils.train.evals.k_fold_cross_validation.KFoldCrossValidation method) (cellmil.utils.train.evals.KFoldCrossValidation method) (cellmil.utils.train.evals.utils.Report method) (cellmil.utils.train.FocalLoss method) (cellmil.utils.train.losses.FocalLoss method) (cellmil.utils.train.losses.NegativeLogLikelihoodSurvLoss method) (cellmil.utils.train.metrics.BrierScore method) (cellmil.utils.train.metrics.ConcordanceIndex method) (cellmil.utils.wandb.ExperimentComponents method) (cellmil.utils.wandb.WandbClient method) (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) __iter__() (cellmil.datamodels.transforms.pipeline.TransformPipeline method) (cellmil.datamodels.transforms.TransformPipeline method) __len__() (cellmil.datamodels.datasets.cell_gnn_mil_dataset.CellGNNMILDataset method) (cellmil.datamodels.datasets.cell_mil_dataset.CellMILDataset method) (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) (cellmil.datamodels.datasets.neoplastic_dataset.NeoplasticDataset method) (cellmil.datamodels.datasets.NeoplasticDataset method) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset method) (cellmil.datamodels.transforms.label_pipeline.LabelTransformPipeline method) (cellmil.datamodels.transforms.LabelTransformPipeline method) (cellmil.datamodels.transforms.pipeline.TransformPipeline method) (cellmil.datamodels.transforms.TransformPipeline method) __post_init__() (cellmil.datamodels.WSI method) (cellmil.datamodels.wsi.WSI method) _add_small_world_edges() (cellmil.models.mil.graphmil.gnn.SmallWorld method) (cellmil.models.mil.graphmil.SmallWorld method) _adjust_perplexity() (cellmil.visualization.feature_visualizer.FeatureVisualizer static method) (cellmil.visualization.FeatureVisualizer static method) _aggregate_reports() (cellmil.utils.train.evals.k_fold_cross_validation.KFoldCrossValidation method) (cellmil.utils.train.evals.KFoldCrossValidation method) _apply_roi_filtering() (cellmil.datamodels.datasets.cell_gnn_mil_dataset.CellGNNMILDataset method) (cellmil.datamodels.datasets.cell_mil_dataset.CellMILDataset method) _are_contour_coordinates_valid() (cellmil.segmentation.cell_segmenter.CellSegmenter method) (cellmil.segmentation.CellSegmenter method) _BatchNormRelu (class in cellmil.models.segmentation.hovernet) _build_path_from_values() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _calculate_anisotropy() (cellmil.features.extractor.topological.GeometricExtractor method) _calculate_convex_hull_features() (cellmil.features.extractor.topological.GeometricExtractor method) _calculate_edge_features() (cellmil.graph.creator.EdgeCreator method) _calculate_ego_network_density() (cellmil.features.extractor.topological.StructureExtractor method) _calculate_first_order_stats() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _calculate_js_divergence_table() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _calculate_local_density() (cellmil.features.extractor.topological.GeometricExtractor method) _calculate_local_efficiency() (cellmil.features.extractor.topological.StructureExtractor method) _calculate_mean_orientation() (cellmil.features.extractor.topological.GeometricExtractor method) _calculate_relative_nucleus_size() (cellmil.features.extractor.topological.GeometricExtractor method) _calculate_safe_batch_size() (cellmil.graph.creator.SimilarityEdgeCreator method) _calculate_spatial_entropy() (cellmil.features.extractor.topological.GeometricExtractor method) _can_load_features() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _ce_loss_nc_head() (in module cellmil.models.segmentation.hovernet) _ce_loss_np_head() (in module cellmil.models.segmentation.hovernet) _cell_type_names_to_indices() (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) _check_config() (cellmil.dataset.dataset_creator.DatasetCreator method) (cellmil.dataset.DatasetCreator method) _check_overwrite() (cellmil.data.patch_extractor.PatchExtractor method) (cellmil.data.PatchExtractor method) _check_patch_params() (cellmil.data.patch_extractor.PatchExtractor static method) (cellmil.data.PatchExtractor static method) _clean_edge_cells() (cellmil.segmentation.cell_segmenter.CellPostProcessor method) _compute_correlation_filter() (cellmil.datamodels.datasets.neoplastic_dataset.NeoplasticDataset method) (cellmil.datamodels.datasets.NeoplasticDataset method) _compute_correlation_matrix() (cellmil.datamodels.transforms.correlation_filter.CorrelationFilterTransform method) (cellmil.datamodels.transforms.CorrelationFilterTransform method) _compute_distance_similarity() (cellmil.graph.creator.SimilarityEdgeCreator method) _compute_feature_similarity() (cellmil.graph.creator.SimilarityEdgeCreator method) _compute_masks() (cellmil.models.segmentation.CellposeSAM method) (cellmil.models.segmentation.cellposeV2.CellposeSAM method) _compute_normalization_params() (cellmil.datamodels.datasets.neoplastic_dataset.NeoplasticDataset method) (cellmil.datamodels.datasets.NeoplasticDataset method) _convert_multiclass_mask_to_binary() (in module cellmil.models.segmentation.hovernet) _convert_outputs_to_tensors() (cellmil.models.segmentation.cellpose.CellposeSAM method) _create_cell_type_unavailable_message() (cellmil.visualization.feature_visualizer.FeatureVisualizer static method) (cellmil.visualization.FeatureVisualizer static method) _create_combined_cell_type_distribution() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _create_combined_distribution_comparison() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _create_combined_pca_by_cell_type() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _create_combined_pca_plot() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _create_combined_tsne_by_cell_type() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _create_combined_tsne_plot() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _create_controls() (cellmil.graph.debug_visualizer.GraphDebugVisualizer method) _create_correlation_matrix() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _create_distribution_comparison_plot() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _create_distribution_plot() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _create_edge_creator() (cellmil.graph.debug_visualizer.GraphDebugVisualizer method) _create_empty_graph() (cellmil.graph.creator.Creator method) _create_error_message() (cellmil.visualization.feature_visualizer.FeatureVisualizer static method) (cellmil.visualization.FeatureVisualizer static method) _create_figure() (cellmil.graph.debug_visualizer.GraphDebugVisualizer method) _create_js_divergence_table_component() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _create_label() (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) _create_neoplastic_labels() (cellmil.datamodels.datasets.neoplastic_dataset.NeoplasticDataset method) (cellmil.datamodels.datasets.NeoplasticDataset method) _create_pca_by_cell_type() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _create_pca_plot() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _create_scatter_by_labels() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _create_stats() (cellmil.graph.debug_visualizer.GraphDebugVisualizer method) _create_stats_table() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _create_tsne_by_cell_type() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _create_tsne_plot() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _dice_loss_nc_head() (in module cellmil.models.segmentation.hovernet) _dice_loss_np_head() (in module cellmil.models.segmentation.hovernet) _download_models() (cellmil.segmentation.cell_segmenter.CellSegmenter method) (cellmil.segmentation.CellSegmenter method) _drop_processed_files() (cellmil.data.patch_extractor.PatchExtractor method) (cellmil.data.PatchExtractor method) _ensure_global_metrics_computed() (cellmil.features.extractor.topological.ConnectivityExtractor method) (cellmil.features.extractor.topological.StructureExtractor method) _ensure_spatial_index() (cellmil.features.extractor.topological.GeometricExtractor method) _estimate_memory_usage() (cellmil.graph.creator.SimilarityEdgeCreator method) _explore_directory() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _extract_contour() (cellmil.models.segmentation.cellpose.CellposeSAM method) (cellmil.models.segmentation.CellposeSAM method) (cellmil.models.segmentation.cellposeV2.CellposeSAM method) _extract_features() (cellmil.dataset.dataset_creator.DatasetCreator method) (cellmil.dataset.DatasetCreator method) _extract_node_features() (cellmil.graph.creator.Creator method) _extract_slide_name() (cellmil.datamodels.datasets.neoplastic_dataset.NeoplasticDataset method) (cellmil.datamodels.datasets.NeoplasticDataset method) _find_features_to_remove() (cellmil.datamodels.transforms.correlation_filter.CorrelationFilterTransform method) (cellmil.datamodels.transforms.CorrelationFilterTransform method) _find_index() (cellmil.features.extractor.topological.ConnectivityExtractor method) (cellmil.features.extractor.topological.GeometricExtractor method) (cellmil.features.extractor.topological.StructureExtractor method) _fit_bayesian_models() (cellmil.statistics.stats_printer.StatsPrinter method) (cellmil.statistics.StatsPrinter method) _fit_frequentist_models() (cellmil.statistics.stats_printer.StatsPrinter method) (cellmil.statistics.StatsPrinter method) _flatten_and_log_metrics() (cellmil.models.mil.clam.LitCLAM method) (cellmil.models.mil.graphmil.LitGraphMIL method) (cellmil.models.mil.LitCLAM method) (cellmil.models.mil.LitGraphMIL method) (cellmil.models.mil.utils.LitGeneral method) _format_bayesian_results() (cellmil.statistics.stats_printer.StatsPrinter method) (cellmil.statistics.StatsPrinter method) _format_frequentist_results() (cellmil.statistics.stats_printer.StatsPrinter method) (cellmil.statistics.StatsPrinter method) _format_params() (cellmil.graph.debug_visualizer.GraphDebugVisualizer method) _forward_upsample() (cellmil.models.segmentation.cellvit.CellViT method) _generate_next_value_() (cellmil.interfaces.AttentionExplainerConfig.Aggregation method) (cellmil.interfaces.AttentionExplainerConfig.Normalization method) (cellmil.interfaces.AttentionExplainerConfig.VisualizationMode method) (cellmil.interfaces.EvaluationExternalValidatorConfig.AggregationMethod method) (cellmil.interfaces.EvaluationExternalValidatorConfig.FinalModel method) (cellmil.interfaces.EvaluationReporterConfig.Metrics method) (cellmil.interfaces.MIL.MILType method) (cellmil.interfaces.MIL.RouteType method) (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerType method) _generate_pdf_from_markdown() (cellmil.statistics.stats_printer.StatsPrinter method) (cellmil.statistics.StatsPrinter method) _generate_report() (cellmil.statistics.stats_printer.StatsPrinter method) (cellmil.statistics.StatsPrinter method) _get_available_gpu_memory() (cellmil.graph.creator.SimilarityEdgeCreator method) _get_available_options_at_level() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _get_available_slides() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _get_cell_mapping() (cellmil.features.extractor.topological.GeometricExtractor method) _get_cell_types_tensor() (cellmil.datamodels.datasets.cell_gnn_mil_dataset.CellGNNMILDataset method) (cellmil.datamodels.datasets.cell_mil_dataset.CellMILDataset method) _get_cells_position() (cellmil.graph.graph_creator.GraphCreator method) (cellmil.graph.GraphCreator method) _get_centroids_tensor() (cellmil.datamodels.datasets.cell_gnn_mil_dataset.CellGNNMILDataset method) _get_classification_report() (cellmil.utils.train.evals.utils.Report method) _get_data_path() (cellmil.datamodels.datasets.cell_mil_dataset.CellMILDataset method) (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) _get_features_path() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _get_gradient_hv() (in module cellmil.models.segmentation.hovernet) _get_labels() (cellmil.datamodels.datasets.cell_gnn_mil_dataset.CellGNNMILDataset method) (cellmil.datamodels.datasets.cell_mil_dataset.CellMILDataset method) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset method) (cellmil.datamodels.datasets.patch_mil_dataset.PatchMILDataset method) _get_magnification_openslide() (cellmil.dataset.dataset_creator.DatasetCreator method) (cellmil.dataset.DatasetCreator method) _get_metadata() (cellmil.datamodels.WSI method) (cellmil.datamodels.wsi.WSI method) _get_morphological_features() (cellmil.features.feature_extractor.FeatureExtractor static method) (cellmil.features.FeatureExtractor static method) _get_neighbors_vectorized() (cellmil.features.extractor.topological.StructureExtractor method) _get_neighbour_data() (cellmil.features.extractor.topological.GeometricExtractor method) _get_patch_path() (cellmil.features.feature_extractor.FeatureExtractor static method) (cellmil.features.FeatureExtractor static method) _get_positions_tensor() (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset method) _get_predictions() (cellmil.utils.train.evals.k_fold_cross_validation.KFoldCrossValidation method) (cellmil.utils.train.evals.KFoldCrossValidation method) _get_processed_path() (cellmil.datamodels.datasets.patch_mil_dataset.PatchMILDataset method) _get_run_config() (cellmil.statistics.stats_printer.StatsPrinter method) (cellmil.statistics.StatsPrinter method) _get_size_args() (cellmil.models.mil.clam.LitCLAM static method) (cellmil.models.mil.LitCLAM static method) _get_slides() (cellmil.datamodels.datasets.cell_gnn_mil_dataset.CellGNNMILDataset method) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset method) _get_specific_hyperparameters() (cellmil.models.mil.graphmil.GlobalPooling_Classifier method) (cellmil.models.mil.graphmil.GNN method) (cellmil.models.mil.graphmil.gnn.GNN method) (cellmil.models.mil.graphmil.pool.GlobalPooling_Classifier method) _get_survival_report() (cellmil.utils.train.evals.utils.Report method) _get_topological_features() (cellmil.features.feature_extractor.FeatureExtractor static method) (cellmil.features.FeatureExtractor static method) _get_wsi_dimensions() (cellmil.segmentation.cell_segmenter.CellSegmenter method) (cellmil.segmentation.CellSegmenter method) _get_wsi_patch_metadata() (cellmil.datamodels.WSI method) (cellmil.datamodels.wsi.WSI method) _graph_key() (cellmil.features.extractor.topological.GeometricExtractor method) _has_dataloader_error() (cellmil.utils.wandb.WandbClient method) _HoverNetDecoder (class in cellmil.models.segmentation.hovernet) _HoVerNetDenseUnit (class in cellmil.models.segmentation.hovernet) _HoVerNetEncoder (class in cellmil.models.segmentation.hovernet) _HoVerNetResidualUnit (class in cellmil.models.segmentation.hovernet) _init_cellpose_network() (cellmil.models.segmentation.CellposeSAM method) (cellmil.models.segmentation.cellposeV2.CellposeSAM method) _is_gated_attention() (cellmil.models.mil.clam.LitCLAM static method) (cellmil.models.mil.LitCLAM static method) _launch_debug_visualizer() (cellmil.graph.graph_creator.GraphCreator method) (cellmil.graph.GraphCreator method) _load_all_metadata() (cellmil.datamodels.model.ModelStorage method) _load_best_model() (cellmil.utils.train.evals.utils.Report method) _load_cell_types() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _load_cells() (cellmil.features.feature_extractor.FeatureExtractor method) (cellmil.features.FeatureExtractor method) (cellmil.graph.graph_creator.GraphCreator method) (cellmil.graph.GraphCreator method) _load_data() (cellmil.datamodels.datasets.cell_mil_dataset.CellMILDataset method) (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) _load_experiment_metadata() (cellmil.datamodels.model.ModelStorage method) _load_features() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _load_fold_metadata() (cellmil.datamodels.model.ModelStorage method) _load_graph() (cellmil.features.feature_extractor.FeatureExtractor method) (cellmil.features.FeatureExtractor method) _load_inference_transforms() (cellmil.segmentation.cell_segmenter.CellSegmenter method) (cellmil.segmentation.CellSegmenter method) _load_metadata() (cellmil.features.feature_extractor.FeatureExtractor method) (cellmil.features.FeatureExtractor method) _load_model() (cellmil.segmentation.cell_segmenter.CellSegmenter method) (cellmil.segmentation.CellSegmenter method) _load_morphological_features() (cellmil.graph.graph_creator.GraphCreator method) (cellmil.graph.GraphCreator method) _load_patch() (cellmil.features.feature_extractor.FeatureExtractor static method) (cellmil.features.FeatureExtractor static method) _load_processed_data() (cellmil.datamodels.datasets.patch_mil_dataset.PatchMILDataset method) _load_progress() (cellmil.dataset.dataset_creator.DatasetCreator method) (cellmil.dataset.DatasetCreator method) _load_slide_features() (cellmil.datamodels.datasets.cell_mil_dataset.CellMILDataset method) _log_class_distribution() (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) _log_epoch_metrics() (cellmil.models.mil.clam.CLAMTrainerLegacy method) _loss_hv_grad() (in module cellmil.models.segmentation.hovernet) _loss_hv_mse() (in module cellmil.models.segmentation.hovernet) _make_HoVerNet_dense_block() (in module cellmil.models.segmentation.hovernet) _make_HoVerNet_residual_block() (in module cellmil.models.segmentation.hovernet) _merge_graph_with_features() (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset method) _normalize_batch() (cellmil.models.segmentation.CellposeSAM method) (cellmil.models.segmentation.cellposeV2.CellposeSAM method) _plot_correlation_matrix() (cellmil.datamodels.transforms.correlation_filter.CorrelationFilterTransform method) (cellmil.datamodels.transforms.CorrelationFilterTransform method) _plot_graph() (cellmil.graph.graph_creator.GraphCreator method) (cellmil.graph.GraphCreator method) _pool_init() (in module cellmil.features.feature_extractor) _post_process_single_hovernet() (in module cellmil.models.segmentation.hovernet) _prepare_combined_data() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _prepare_combined_data_with_cell_types() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _prepare_data() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _prepare_data_with_cell_types() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _prepare_wsi() (cellmil.data.patch_extractor.PatchExtractor method) (cellmil.data.PatchExtractor method) _preprocess() (cellmil.features.extractor.morphological.PyRadiomicsExtractor method) _preprocess_excel() (cellmil.dataset.dataset_creator.DatasetCreator method) (cellmil.dataset.DatasetCreator method) _preprocess_row_for_neoplastic() (cellmil.datamodels.datasets.neoplastic_dataset.NeoplasticDataset method) (cellmil.datamodels.datasets.NeoplasticDataset method) _preprocess_slide_features() (cellmil.datamodels.datasets.patch_mil_dataset.PatchMILDataset method) _process_batched() (cellmil.graph.creator.EdgeCreator method) _process_dataset() (cellmil.datamodels.datasets.cell_mil_dataset.CellMILDataset method) (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) (cellmil.datamodels.datasets.patch_mil_dataset.PatchMILDataset method) _process_label_smoothing() (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) _process_single_graph() (cellmil.datamodels.datasets.cell_gnn_mil_dataset.CellGNNMILDataset method) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset method) _process_slide() (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) _read_data() (cellmil.datamodels.datasets.neoplastic_dataset.NeoplasticDataset method) (cellmil.datamodels.datasets.NeoplasticDataset method) _read_excel() (cellmil.dataset.dataset_creator.DatasetCreator method) (cellmil.dataset.DatasetCreator method) _remove_overlap() (cellmil.segmentation.cell_segmenter.CellPostProcessor method) _resize_cellprob_batch() (cellmil.models.segmentation.CellposeSAM method) (cellmil.models.segmentation.cellposeV2.CellposeSAM method) _resize_flows_batch() (cellmil.models.segmentation.CellposeSAM method) (cellmil.models.segmentation.cellposeV2.CellposeSAM method) _results_to_tensor() (cellmil.features.feature_extractor.FeatureExtractor method) (cellmil.features.FeatureExtractor method) _sample_data() (cellmil.visualization.feature_visualizer.FeatureVisualizer static method) (cellmil.visualization.FeatureVisualizer static method) _save_data() (cellmil.datamodels.datasets.cell_mil_dataset.CellMILDataset method) (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) _save_graph() (cellmil.graph.graph_creator.GraphCreator method) (cellmil.graph.GraphCreator method) _save_processed_data() (cellmil.datamodels.datasets.patch_mil_dataset.PatchMILDataset method) _save_pt() (cellmil.features.feature_extractor.FeatureExtractor method) (cellmil.features.FeatureExtractor method) _set_hardware() (cellmil.data.patch_extractor.PatchExtractor method) (cellmil.data.PatchExtractor method) _set_wsi_path() (cellmil.data.patch_extractor.PatchExtractor method) (cellmil.data.PatchExtractor method) _setup_callbacks() (cellmil.graph.debug_visualizer.GraphDebugVisualizer method) _setup_layout() (cellmil.graph.debug_visualizer.GraphDebugVisualizer method) _setup_metrics() (cellmil.models.mil.attentiondeepmil.LitSurvAttentionDeepMIL method) (cellmil.models.mil.cellconv.LitSurvCellConv method) (cellmil.models.mil.clam.LitSurvCLAM method) (cellmil.models.mil.graphmil.LitSurvGraphMIL method) (cellmil.models.mil.head4type.LitSurvHead4Type method) _setup_sync_callbacks() (cellmil.graph.debug_visualizer.GraphDebugVisualizer method) _setup_wsi() (cellmil.segmentation.cell_segmenter.CellSegmenter method) (cellmil.segmentation.CellSegmenter method) _stack_batch_results() (cellmil.models.segmentation.cellpose.CellposeSAM method) _standardize_and_fit_pca() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _standardize_and_fit_tsne() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) _subsample_graph() (cellmil.models.mil.graphmil.LitGraphMIL method) (cellmil.models.mil.LitGraphMIL method) _to_numpy() (cellmil.visualization.feature_visualizer.FeatureVisualizer static method) (cellmil.visualization.FeatureVisualizer static method) _train_epoch() (cellmil.models.mil.clam.CLAMTrainerLegacy method) _train_final_model() (cellmil.utils.train.evals.k_fold_cross_validation.KFoldCrossValidation method) (cellmil.utils.train.evals.KFoldCrossValidation method) _transform_impl() (cellmil.datamodels.transforms.base_transform.FittableTransform method) (cellmil.datamodels.transforms.correlation_filter.CorrelationFilterTransform method) (cellmil.datamodels.transforms.CorrelationFilterTransform method) (cellmil.datamodels.transforms.FittableTransform method) (cellmil.datamodels.transforms.normalization.RobustScalerTransform method) (cellmil.datamodels.transforms.RobustScalerTransform method) _transform_labels_impl() (cellmil.datamodels.transforms.base_label_transform.FittableLabelTransform method) (cellmil.datamodels.transforms.FittableLabelTransform method) (cellmil.datamodels.transforms.time_discretizer.TimeDiscretizerTransform method) (cellmil.datamodels.transforms.TimeDiscretizerTransform method) _val() (cellmil.models.mil.clam.CLAMTrainerLegacy method) _validate_features() (cellmil.datamodels.datasets.neoplastic_dataset.NeoplasticDataset method) (cellmil.datamodels.datasets.NeoplasticDataset method) _validate_positive_int() (cellmil.visualization.feature_visualizer.FeatureVisualizer static method) (cellmil.visualization.FeatureVisualizer static method) A accuracy (cellmil.interfaces.EvaluationReporterConfig.Metrics attribute) Accuracy_Logger (class in cellmil.models.mil.utils) add_transform() (cellmil.datamodels.transforms.pipeline.TransformPipeline method) (cellmil.datamodels.transforms.TransformPipeline method) AEM (class in cellmil.models.mil.utils) aggregated_metrics (cellmil.datamodels.model.ExperimentMetadata attribute) Aggregation (class in cellmil.interfaces.AttentionExplainerConfig) aggregation_method (cellmil.interfaces.EvaluationExternalValidatorConfig.EvaluationExternalValidatorConfig attribute) AggregationMethod (class in cellmil.interfaces.EvaluationExternalValidatorConfig) all (cellmil.interfaces.AttentionExplainerConfig.VisualizationMode attribute) all_patch_metadata (cellmil.datamodels.WSI attribute) (cellmil.datamodels.wsi.WSI attribute) apply_permutation() (in module cellmil.datamodels.datasets.utils) arbitrary_types_allowed (cellmil.interfaces.CellSegmenterConfig.Config attribute), [1] (cellmil.interfaces.EvaluationExternalValidatorConfig.EvaluationExternalValidatorConfig.Config attribute) (cellmil.interfaces.EvaluationReporterConfig.EvaluationReporterConfig.Config attribute) (cellmil.interfaces.FeatureExtractorConfig.Config attribute), [1] (cellmil.interfaces.FeatureVisualizerConfig.Config attribute), [1] (cellmil.interfaces.GraphCreatorConfig.Config attribute), [1] (cellmil.interfaces.MILPredictorConfig.Config attribute), [1] (cellmil.interfaces.MILTrainerConfig.Config attribute), [1] (cellmil.interfaces.PatchExtractorConfig.Config attribute), [1] (cellmil.interfaces.StatsPrinterConfig.StatsPrinterConfig.Config attribute) attention (cellmil.interfaces.MIL.MILType attribute) Attention (class in cellmil.models.mil.graphmil) (class in cellmil.models.mil.graphmil.pool) (class in cellmil.models.mil.histobistro) attention_aggregation (cellmil.interfaces.AttentionExplainerConfig.AttentionExplainerConfig attribute) attention_head (cellmil.interfaces.AttentionExplainerConfig.AttentionExplainerConfig attribute) AttentionDeepMIL (class in cellmil.models.mil.attentiondeepmil) AttentionExplainerConfig (class in cellmil.interfaces.AttentionExplainerConfig) Attn_Net (class in cellmil.models.mil.clam) Attn_Net_Gated (class in cellmil.models.mil.clam) auroc (cellmil.interfaces.EvaluationReporterConfig.Metrics attribute) avg_best_epoch (cellmil.datamodels.model.ExperimentMetadata attribute) B background_percentage (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig attribute) balance_cell_counts (cellmil.datamodels.model.ExperimentMetadata attribute) base_run_config (cellmil.statistics.stats_printer.StatsPrinter attribute) baseline_features (cellmil.interfaces.TableConfig.TableConfig attribute) batch_size (cellmil.graph.creator.EdgeCreator attribute) (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig attribute) best_epoch (cellmil.datamodels.model.FoldMetadata attribute) best_fold_idx (cellmil.datamodels.model.ExperimentMetadata attribute) best_metric_value (cellmil.datamodels.model.FoldMetadata attribute) BrierScore (class in cellmil.utils.train.metrics) C c_index (cellmil.interfaces.EvaluationReporterConfig.Metrics attribute) calculate_error() (cellmil.models.mil.clam.CLAMTrainerLegacy static method) (cellmil.models.mil.clam.LitCLAM static method) (cellmil.models.mil.graphmil.LitGraphMIL static method) (cellmil.models.mil.LitCLAM static method) (cellmil.models.mil.LitGraphMIL static method) calculate_instance_map() (cellmil.models.segmentation.cellpose.CellposeSAM method) (cellmil.models.segmentation.CellposeSAM method) (cellmil.models.segmentation.cellposeV2.CellposeSAM method) (cellmil.models.segmentation.cellvit.CellViT method) (cellmil.models.segmentation.HoVerNet method) (cellmil.models.segmentation.hovernet.HoVerNet method) caption (cellmil.interfaces.TableConfig.TableConfig attribute) cell_balance_bins (cellmil.datamodels.model.ExperimentMetadata attribute) cell_segmentation() (in module cellmil.cli.cell_segmentation) cell_type (cellmil.interfaces.MILTrainerConfig attribute), [1] cell_type_name_to_index() (in module cellmil.datamodels.datasets.utils) cell_types_to_tensor() (in module cellmil.datamodels.datasets.utils) CellConv (class in cellmil.models.mil.cellconv) CellGNNMILDataset (class in cellmil.datamodels.datasets.cell_gnn_mil_dataset) cellmil.cli module cellmil.cli.cell_segmentation module cellmil.cli.dataset_creation module cellmil.cli.eval_external module cellmil.cli.eval_report module cellmil.cli.feature_extraction module cellmil.cli.graph_creation module cellmil.cli.patch_extraction module cellmil.cli.stats_print module cellmil.cli.visualize_features module cellmil.config.python module cellmil.config.python.config module cellmil.data module cellmil.data.cucim_deepzoom module cellmil.data.patch_extractor module cellmil.data.storage module cellmil.datamodels module cellmil.datamodels.datasets module cellmil.datamodels.datasets.cell_gnn_mil_dataset module cellmil.datamodels.datasets.cell_mil_dataset module cellmil.datamodels.datasets.celltype_dataset module cellmil.datamodels.datasets.gnn_mil_dataset module cellmil.datamodels.datasets.mil_dataset module cellmil.datamodels.datasets.neoplastic_dataset module cellmil.datamodels.datasets.patch_gnn_mil_dataset module cellmil.datamodels.datasets.patch_mil_dataset module cellmil.datamodels.datasets.utils module cellmil.datamodels.model module cellmil.datamodels.transforms module cellmil.datamodels.transforms.base_label_transform module cellmil.datamodels.transforms.base_transform module cellmil.datamodels.transforms.correlation_filter module cellmil.datamodels.transforms.label_pipeline module cellmil.datamodels.transforms.normalization module cellmil.datamodels.transforms.pipeline module cellmil.datamodels.transforms.time_discretizer module cellmil.datamodels.wsi module cellmil.dataset module cellmil.dataset.dataset_creator module cellmil.features module cellmil.features.extractor module cellmil.features.extractor.embedding module cellmil.features.extractor.morphological module cellmil.features.extractor.topological module cellmil.features.feature_extractor module cellmil.graph module cellmil.graph.creator module cellmil.graph.debug_visualizer module cellmil.graph.graph_creator module cellmil.interfaces module cellmil.interfaces.AttentionExplainerConfig module cellmil.interfaces.EvaluationExternalValidatorConfig module cellmil.interfaces.EvaluationReporterConfig module cellmil.interfaces.MIL module cellmil.interfaces.SHAPExplainerConfig module cellmil.interfaces.StatsPrinterConfig module cellmil.interfaces.TableConfig module cellmil.models module cellmil.models.mil module cellmil.models.mil.attentiondeepmil module cellmil.models.mil.cellconv module cellmil.models.mil.clam module cellmil.models.mil.graphmil module cellmil.models.mil.graphmil.gnn module cellmil.models.mil.graphmil.pool module cellmil.models.mil.head4type module cellmil.models.mil.histobistro module cellmil.models.mil.multifocus module cellmil.models.mil.standard module cellmil.models.mil.transmil module cellmil.models.mil.utils module cellmil.models.segmentation module cellmil.models.segmentation.cellpose module cellmil.models.segmentation.cellposeV2 module cellmil.models.segmentation.cellvit module cellmil.models.segmentation.hovernet module cellmil.segmentation module cellmil.segmentation.cell_segmenter module cellmil.statistics module cellmil.statistics.stats_printer module cellmil.utils module cellmil.utils.dataset_from_dataset module cellmil.utils.stain_normalization module cellmil.utils.templates module cellmil.utils.tools module cellmil.utils.train module cellmil.utils.train.callbacks module cellmil.utils.train.dataset module cellmil.utils.train.evals module cellmil.utils.train.evals.k_fold_cross_validation module cellmil.utils.train.evals.utils module cellmil.utils.train.losses module cellmil.utils.train.metrics module cellmil.utils.wandb module cellmil.visualization module cellmil.visualization.feature_visualizer module CellMILDataset (class in cellmil.datamodels.datasets.cell_mil_dataset) CellposeSAM (class in cellmil.models.segmentation) (class in cellmil.models.segmentation.cellpose) (class in cellmil.models.segmentation.cellposeV2) CellPostProcessor (class in cellmil.segmentation.cell_segmenter) CellSegmenter (class in cellmil.segmentation) (class in cellmil.segmentation.cell_segmenter) CellSegmenterConfig (class in cellmil.interfaces), [1] CellSegmenterConfig.Config (class in cellmil.interfaces), [1] CellTypeDataset (class in cellmil.datamodels.datasets) (class in cellmil.datamodels.datasets.celltype_dataset) CellViT (class in cellmil.models.segmentation.cellvit) CellViTSAM (class in cellmil.models.segmentation) (class in cellmil.models.segmentation.cellvit) centroids_to_tensor() (in module cellmil.datamodels.datasets.utils) CHIMERA (class in cellmil.models.mil.graphmil) (class in cellmil.models.mil.graphmil.gnn) CHIMERA_block (class in cellmil.models.mil.graphmil.gnn) chkpt_path (cellmil.interfaces.MILPredictorConfig attribute), [1] ckpt_path (cellmil.interfaces.MILTrainerConfig attribute), [1] clam (cellmil.interfaces.MIL.MILType attribute) CLAM (class in cellmil.models.mil.graphmil) (class in cellmil.models.mil.graphmil.pool) CLAM_MB (class in cellmil.models.mil.clam) CLAM_SB (class in cellmil.models.mil.clam) CLAMTrainerLegacy (class in cellmil.models.mil.clam) class_index (cellmil.interfaces.AttentionExplainerConfig.AttentionExplainerConfig attribute) classification_metrics (cellmil.interfaces.TableConfig.TableConfig attribute) clean_up() (cellmil.data.storage.Storage method) clear_cache() (cellmil.features.extractor.topological.ConnectivityExtractor method) (cellmil.features.extractor.topological.GeometricExtractor method) (cellmil.features.extractor.topological.StructureExtractor method) close_logger() (in module cellmil.utils.tools) color_scheme (cellmil.interfaces.AttentionExplainerConfig.AttentionExplainerConfig attribute) COLUMN_EXPERIMENT_ID (cellmil.statistics.stats_printer.StatsPrinter attribute) (cellmil.statistics.StatsPrinter attribute) column_sanity_check() (in module cellmil.datamodels.datasets.utils) COLUMN_TASK (cellmil.statistics.stats_printer.StatsPrinter attribute) (cellmil.statistics.StatsPrinter attribute) command line option --dataset --excel_path --extractor --extractors --gpu, [1] --graph_methods --model --output_path, [1] --patch_overlap --patch_size --patched_slide_path, [1] --segmentation_model --segmentation_models --target_mag --wsi_path, [1], [2] connectivity delaunay_radius dilate} geometric gigapath gpu: method morphometrics patched_slide_path plot pyradiomics_hed pyradiomics_hue radius resnet50 uni} complementary_frequencies() (in module cellmil.utils.train.dataset) compute() (cellmil.utils.train.metrics.BrierScore method) (cellmil.utils.train.metrics.ConcordanceIndex method) compute_hv_map() (in module cellmil.models.segmentation.hovernet) compute_normalization() (in module cellmil.datamodels.datasets.utils) compute_slide_cell_counts() (in module cellmil.utils.train.evals.utils) ConcordanceIndex (class in cellmil.utils.train.metrics) configure_optimizers() (cellmil.models.mil.clam.LitCLAM method) (cellmil.models.mil.graphmil.LitGraphMIL method) (cellmil.models.mil.LitCLAM method) (cellmil.models.mil.LitGraphMIL method) (cellmil.models.mil.utils.LitGeneral method) connectivity command line option ConnectivityExtractor (class in cellmil.features.extractor.topological) convert_numpy_types() (in module cellmil.datamodels.model) correlation_filter (cellmil.interfaces.MILTrainerConfig attribute), [1] correlation_filter() (in module cellmil.datamodels.datasets.utils) CorrelationFilterTransform (class in cellmil.datamodels.transforms) (class in cellmil.datamodels.transforms.correlation_filter) cpu() (cellmil.models.segmentation.cellpose.CellposeSAM method) (cellmil.models.segmentation.CellposeSAM method) (cellmil.models.segmentation.cellposeV2.CellposeSAM method) create() (cellmil.dataset.dataset_creator.DatasetCreator method) (cellmil.dataset.DatasetCreator method) (cellmil.features.extractor.Extractor static method) (cellmil.graph.creator.Creator method) (cellmil.statistics.stats_printer.StatsPrinter method) (cellmil.statistics.StatsPrinter method) create_cell_mask() (cellmil.features.feature_extractor.FeatureExtractor static method) (cellmil.features.FeatureExtractor static method) create_color_gradient() (in module cellmil.utils.tools) create_dataset() (in module cellmil.cli.dataset_creation) create_edges() (cellmil.graph.creator.DelaunayEdgeCreator method) (cellmil.graph.creator.DilateEdgeCreator method) (cellmil.graph.creator.EdgeCreator method) (cellmil.graph.creator.KNNEdgeCreator method) (cellmil.graph.creator.RadiusEdgeCreator method) (cellmil.graph.creator.SimilarityEdgeCreator method) create_graph() (cellmil.graph.graph_creator.GraphCreator method) (cellmil.graph.GraphCreator method) create_negative_targets() (cellmil.models.mil.clam.CLAM_SB static method) create_positive_targets() (cellmil.models.mil.clam.CLAM_SB static method) create_processed_dataset_files() (in module cellmil.utils.dataset_from_dataset) create_subset() (cellmil.datamodels.datasets.cell_gnn_mil_dataset.CellGNNMILDataset method) (cellmil.datamodels.datasets.cell_mil_dataset.CellMILDataset method) (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset method) (cellmil.datamodels.datasets.patch_mil_dataset.PatchMILDataset method) create_summary_plots (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig attribute) create_train_val_datasets() (cellmil.datamodels.datasets.cell_gnn_mil_dataset.CellGNNMILDataset method) (cellmil.datamodels.datasets.cell_mil_dataset.CellMILDataset method) (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset method) (cellmil.datamodels.datasets.patch_mil_dataset.PatchMILDataset method) create_train_val_datasets_by_slides() (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) create_upsampling_branch() (cellmil.models.segmentation.cellvit.CellViT method) Creator (class in cellmil.graph.creator) cuda() (cellmil.models.segmentation.cellpose.CellposeSAM method) (cellmil.models.segmentation.CellposeSAM method) (cellmil.models.segmentation.cellposeV2.CellposeSAM method) D dataset (cellmil.interfaces.FeatureVisualizerConfig attribute), [1] dataset_config (cellmil.datamodels.model.ExperimentMetadata attribute) dataset_dir (cellmil.interfaces.EvaluationExternalValidatorConfig.EvaluationExternalValidatorConfig attribute) DatasetCreator (class in cellmil.dataset) (class in cellmil.dataset.dataset_creator) DatasetCreatorConfig (class in cellmil.interfaces), [1] debug (cellmil.interfaces.GraphCreatorConfig attribute), [1] deep (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerType attribute) DeepZoomGeneratorCucim (class in cellmil.data.cucim_deepzoom) delaunay_radius command line option DelaunayEdgeCreator (class in cellmil.graph.creator) device (cellmil.graph.creator.EdgeCreator attribute) DilateEdgeCreator (class in cellmil.graph.creator) dilate} command line option dilation (cellmil.graph.creator.EdgeCreator attribute) download() (cellmil.datamodels.datasets.cell_gnn_mil_dataset.CellGNNMILDataset method) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset method) dp_metadata_file (cellmil.interfaces.EvaluationExternalValidatorConfig.EvaluationExternalValidatorConfig attribute) E EarlyStopping (class in cellmil.models.mil.utils) EdgeCreator (class in cellmil.graph.creator) EGNN (class in cellmil.models.mil.graphmil) (class in cellmil.models.mil.graphmil.gnn) embedding_name (cellmil.datamodels.WSI attribute) (cellmil.datamodels.wsi.WSI attribute) EmbeddingExtractor (class in cellmil.features.extractor.embedding) end_timer() (in module cellmil.utils.tools) ensemble (cellmil.interfaces.EvaluationExternalValidatorConfig.FinalModel attribute) eval() (cellmil.models.mil.clam.CLAMTrainerLegacy method) (cellmil.models.segmentation.cellpose.CellposeSAM method) (cellmil.models.segmentation.CellposeSAM method) (cellmil.models.segmentation.cellposeV2.CellposeSAM method) eval_external() (in module cellmil.cli.eval_external) eval_report() (in module cellmil.cli.eval_report) evaluate() (cellmil.utils.train.evals.k_fold_cross_validation.KFoldCrossValidation method) (cellmil.utils.train.evals.KFoldCrossValidation method) EvaluationExternalValidatorConfig (class in cellmil.interfaces.EvaluationExternalValidatorConfig) EvaluationExternalValidatorConfig.Config (class in cellmil.interfaces.EvaluationExternalValidatorConfig) EvaluationReporterConfig (class in cellmil.interfaces.EvaluationReporterConfig) EvaluationReporterConfig.Config (class in cellmil.interfaces.EvaluationReporterConfig) everything (cellmil.interfaces.EvaluationExternalValidatorConfig.AggregationMethod attribute) excel_path (cellmil.interfaces.DatasetCreatorConfig attribute), [1] (cellmil.interfaces.MILTrainerConfig attribute), [1] ExperimentComponents (class in cellmil.utils.wandb) ExperimentMetadata (class in cellmil.datamodels.model) explain_mean_head (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig attribute) explain_per_head (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig attribute) explain_top_cells (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig attribute) explainer_type (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig attribute) extract_features() (cellmil.features.extractor.embedding.EmbeddingExtractor method) (cellmil.features.extractor.embedding.GigapathExtractor method) (cellmil.features.extractor.embedding.ResNet50Extractor method) (cellmil.features.extractor.embedding.UNIExtractor method) (cellmil.features.extractor.morphological.MorphologicalExtractor method) (cellmil.features.extractor.morphological.MorphometricsExtractor method) (cellmil.features.extractor.morphological.PyRadiomicsExtractor method) (cellmil.features.extractor.topological.ConnectivityExtractor method) (cellmil.features.extractor.topological.GeometricExtractor method) (cellmil.features.extractor.topological.StructureExtractor method) (cellmil.features.extractor.topological.TopologicalExtractor method) extract_nuclei_info() (in module cellmil.models.segmentation.hovernet) extract_slide_name() (in module cellmil.datamodels.datasets.utils) extractor (cellmil.interfaces.FeatureExtractorConfig attribute), [1] (cellmil.interfaces.MILPredictorConfig attribute), [1] (cellmil.interfaces.MILTrainerConfig attribute), [1] Extractor (class in cellmil.features.extractor) extractors (cellmil.interfaces.DatasetCreatorConfig attribute), [1] F f1 (cellmil.interfaces.EvaluationReporterConfig.Metrics attribute) feature_extraction() (in module cellmil.cli.feature_extraction) feature_mapping (cellmil.interfaces.TableConfig.TableConfig attribute) FeatureExtractor (class in cellmil.features) (class in cellmil.features.feature_extractor) FeatureExtractorConfig (class in cellmil.interfaces), [1] FeatureExtractorConfig.Config (class in cellmil.interfaces), [1] features (cellmil.interfaces.TableConfig.TableConfig attribute) (cellmil.utils.wandb.ExperimentComponents attribute) FEATURES_KEY (cellmil.statistics.stats_printer.StatsPrinter attribute) (cellmil.statistics.StatsPrinter attribute) FeatureVisualizer (class in cellmil.visualization) (class in cellmil.visualization.feature_visualizer) FeatureVisualizerConfig (class in cellmil.interfaces), [1] FeatureVisualizerConfig.Config (class in cellmil.interfaces), [1] FeedForward (class in cellmil.models.mil.histobistro) filter_cells_by_roi() (in module cellmil.datamodels.datasets.utils) filter_split() (in module cellmil.datamodels.datasets.utils) final (cellmil.interfaces.EvaluationExternalValidatorConfig.FinalModel attribute) final_model (cellmil.interfaces.EvaluationExternalValidatorConfig.EvaluationExternalValidatorConfig attribute) FinalModel (class in cellmil.interfaces.EvaluationExternalValidatorConfig) fit() (cellmil.datamodels.transforms.base_label_transform.FittableLabelTransform method) (cellmil.datamodels.transforms.base_transform.FittableTransform method) (cellmil.datamodels.transforms.correlation_filter.CorrelationFilterTransform method) (cellmil.datamodels.transforms.CorrelationFilterTransform method) (cellmil.datamodels.transforms.FittableLabelTransform method) (cellmil.datamodels.transforms.FittableTransform method) (cellmil.datamodels.transforms.label_pipeline.LabelTransformPipeline method) (cellmil.datamodels.transforms.LabelTransformPipeline method) (cellmil.datamodels.transforms.normalization.RobustScalerTransform method) (cellmil.datamodels.transforms.pipeline.TransformPipeline method) (cellmil.datamodels.transforms.RobustScalerTransform method) (cellmil.datamodels.transforms.time_discretizer.TimeDiscretizerTransform method) (cellmil.datamodels.transforms.TimeDiscretizerTransform method) (cellmil.datamodels.transforms.TransformPipeline method) (cellmil.models.mil.clam.CLAMTrainerLegacy method) fit_transform() (cellmil.datamodels.transforms.base_label_transform.FittableLabelTransform method) (cellmil.datamodels.transforms.base_transform.FittableTransform method) (cellmil.datamodels.transforms.FittableLabelTransform method) (cellmil.datamodels.transforms.FittableTransform method) (cellmil.datamodels.transforms.label_pipeline.LabelTransformPipeline method) (cellmil.datamodels.transforms.LabelTransformPipeline method) (cellmil.datamodels.transforms.pipeline.TransformPipeline method) (cellmil.datamodels.transforms.TransformPipeline method) FittableLabelTransform (class in cellmil.datamodels.transforms) (class in cellmil.datamodels.transforms.base_label_transform) FittableTransform (class in cellmil.datamodels.transforms) (class in cellmil.datamodels.transforms.base_transform) FocalLoss (class in cellmil.utils.train) (class in cellmil.utils.train.losses) fold_idx (cellmil.datamodels.model.FoldMetadata attribute) folder (cellmil.interfaces.MILTrainerConfig attribute), [1] FoldMetadata (class in cellmil.datamodels.model) forward() (cellmil.models.mil.attentiondeepmil.AttentionDeepMIL method) (cellmil.models.mil.attentiondeepmil.LitAttentionDeepMIL method) (cellmil.models.mil.cellconv.CellConv method) (cellmil.models.mil.cellconv.LitCellConv method) (cellmil.models.mil.clam.Attn_Net method) (cellmil.models.mil.clam.Attn_Net_Gated method) (cellmil.models.mil.clam.CLAM_MB method) (cellmil.models.mil.clam.CLAM_SB method) (cellmil.models.mil.clam.LitCLAM method) (cellmil.models.mil.graphmil.Attention method) (cellmil.models.mil.graphmil.CHIMERA method) (cellmil.models.mil.graphmil.CLAM method) (cellmil.models.mil.graphmil.EGNN method) (cellmil.models.mil.graphmil.GlobalPooling_Classifier method) (cellmil.models.mil.graphmil.GNN method) (cellmil.models.mil.graphmil.gnn.CHIMERA method) (cellmil.models.mil.graphmil.gnn.CHIMERA_block method) (cellmil.models.mil.graphmil.gnn.EGNN method) (cellmil.models.mil.graphmil.gnn.GNN method) (cellmil.models.mil.graphmil.gnn.SGFormer method) (cellmil.models.mil.graphmil.gnn.SGFormerAttention method) (cellmil.models.mil.graphmil.gnn.SmallWorld method) (cellmil.models.mil.graphmil.LitGraphMIL method) (cellmil.models.mil.graphmil.Mean_MLP method) (cellmil.models.mil.graphmil.pool.Attention method) (cellmil.models.mil.graphmil.pool.CLAM method) (cellmil.models.mil.graphmil.pool.GlobalPooling_Classifier method) (cellmil.models.mil.graphmil.pool.Mean_MLP method) (cellmil.models.mil.graphmil.pool.Standard method) (cellmil.models.mil.graphmil.SGFormer method) (cellmil.models.mil.graphmil.SmallWorld method) (cellmil.models.mil.graphmil.Standard method) (cellmil.models.mil.head4type.Head4Type method) (cellmil.models.mil.head4type.LitHead4Type method) (cellmil.models.mil.histobistro.Attention method) (cellmil.models.mil.histobistro.FeedForward method) (cellmil.models.mil.histobistro.HistoBistro method) (cellmil.models.mil.histobistro.PreNorm method) (cellmil.models.mil.histobistro.TransformerBlocks method) (cellmil.models.mil.LitAttentionDeepMIL method) (cellmil.models.mil.LitCLAM method) (cellmil.models.mil.LitGraphMIL method) (cellmil.models.mil.LitStandard method) (cellmil.models.mil.multifocus.LitMultiFocus method) (cellmil.models.mil.multifocus.MultiFocus method) (cellmil.models.mil.standard.LitStandard method) (cellmil.models.mil.standard.MIL_fc method) (cellmil.models.mil.standard.MIL_fc_mc method) (cellmil.models.mil.transmil.PPEG method) (cellmil.models.mil.transmil.TransLayer method) (cellmil.models.mil.transmil.TransMIL method) (cellmil.models.mil.utils.LitGeneral method) (cellmil.models.segmentation.cellpose.CellposeSAM method) (cellmil.models.segmentation.CellposeSAM method) (cellmil.models.segmentation.cellposeV2.CellposeSAM method) (cellmil.models.segmentation.cellvit.CellViT method) (cellmil.models.segmentation.cellvit.CellViTSAM method) (cellmil.models.segmentation.CellViTSAM method) (cellmil.models.segmentation.HoVerNet method) (cellmil.models.segmentation.hovernet._BatchNormRelu method) (cellmil.models.segmentation.hovernet._HoverNetDecoder method) (cellmil.models.segmentation.hovernet._HoVerNetDenseUnit method) (cellmil.models.segmentation.hovernet._HoVerNetEncoder method) (cellmil.models.segmentation.hovernet._HoVerNetResidualUnit method) (cellmil.models.segmentation.hovernet.HoVerNet method) (cellmil.utils.train.FocalLoss method) (cellmil.utils.train.losses.FocalLoss method) freeze_encoder() (cellmil.models.segmentation.cellvit.CellViT method) from_config() (cellmil.datamodels.transforms.base_label_transform.LabelTransform class method) (cellmil.datamodels.transforms.base_transform.Transform class method) (cellmil.datamodels.transforms.correlation_filter.CorrelationFilterTransform class method) (cellmil.datamodels.transforms.CorrelationFilterTransform class method) (cellmil.datamodels.transforms.LabelTransform class method) (cellmil.datamodels.transforms.normalization.RobustScalerTransform class method) (cellmil.datamodels.transforms.RobustScalerTransform class method) (cellmil.datamodels.transforms.time_discretizer.TimeDiscretizerTransform class method) (cellmil.datamodels.transforms.TimeDiscretizerTransform class method) (cellmil.datamodels.transforms.Transform class method) from_directory() (cellmil.datamodels.model.ModelStorage class method) full_state_update (cellmil.utils.train.metrics.BrierScore attribute) (cellmil.utils.train.metrics.ConcordanceIndex attribute) G GAT (class in cellmil.models.mil.graphmil) (class in cellmil.models.mil.graphmil.gnn) GATv2 (class in cellmil.models.mil.graphmil) (class in cellmil.models.mil.graphmil.gnn) generate() (cellmil.utils.train.evals.utils.Report method) generate_instance_nuclei_map() (cellmil.models.segmentation.cellvit.CellViT method) geojson (cellmil.interfaces.AttentionExplainerConfig.VisualizationMode attribute) geometric command line option GeometricExtractor (class in cellmil.features.extractor.topological) get() (cellmil.datamodels.datasets.cell_gnn_mil_dataset.CellGNNMILDataset method) (cellmil.datamodels.datasets.cell_gnn_mil_dataset.SubsetCellGNNMILDataset method) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset method) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.SubsetPatchGNNMILDataset method) get_aem() (cellmil.models.mil.utils.AEM method) get_attention_map() (cellmil.models.mil.histobistro.Attention method) get_attention_weights() (cellmil.models.mil.attentiondeepmil.LitAttentionDeepMIL method) (cellmil.models.mil.cellconv.LitCellConv method) (cellmil.models.mil.clam.LitCLAM method) (cellmil.models.mil.graphmil.Attention method) (cellmil.models.mil.graphmil.CLAM method) (cellmil.models.mil.graphmil.GAT method) (cellmil.models.mil.graphmil.GATv2 method) (cellmil.models.mil.graphmil.GlobalPooling_Classifier method) (cellmil.models.mil.graphmil.GNN method) (cellmil.models.mil.graphmil.gnn.GAT method) (cellmil.models.mil.graphmil.gnn.GATv2 method) (cellmil.models.mil.graphmil.gnn.GNN method) (cellmil.models.mil.graphmil.LitGraphMIL method) (cellmil.models.mil.graphmil.pool.Attention method) (cellmil.models.mil.graphmil.pool.CLAM method) (cellmil.models.mil.graphmil.pool.GlobalPooling_Classifier method) (cellmil.models.mil.head4type.LitHead4Type method) (cellmil.models.mil.LitAttentionDeepMIL method) (cellmil.models.mil.LitCLAM method) (cellmil.models.mil.LitGraphMIL method) (cellmil.models.mil.multifocus.LitMultiFocus method) get_attn_gradients() (cellmil.models.mil.histobistro.Attention method) get_average_best_epoch() (cellmil.datamodels.model.ModelStorage method) get_cell_detection_path() (in module cellmil.datamodels.datasets.utils) get_cell_features() (in module cellmil.datamodels.datasets.utils) get_cell_position() (in module cellmil.segmentation.cell_segmenter) get_cell_position_marging() (in module cellmil.segmentation.cell_segmenter) get_cell_predictions() (cellmil.segmentation.cell_segmenter.CellSegmenter method) (cellmil.segmentation.CellSegmenter method) get_cell_types() (in module cellmil.datamodels.datasets.utils) get_centroids() (in module cellmil.datamodels.datasets.utils) get_class_distribution() (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) (cellmil.datamodels.datasets.neoplastic_dataset.NeoplasticDataset method) (cellmil.datamodels.datasets.NeoplasticDataset method) get_config() (cellmil.datamodels.datasets.cell_gnn_mil_dataset.CellGNNMILDataset method) (cellmil.datamodels.datasets.cell_mil_dataset.CellMILDataset method) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset method) (cellmil.datamodels.datasets.patch_mil_dataset.PatchMILDataset method) (cellmil.datamodels.transforms.base_label_transform.LabelTransform method) (cellmil.datamodels.transforms.base_transform.Transform method) (cellmil.datamodels.transforms.correlation_filter.CorrelationFilterTransform method) (cellmil.datamodels.transforms.CorrelationFilterTransform method) (cellmil.datamodels.transforms.label_pipeline.LabelTransformPipeline method) (cellmil.datamodels.transforms.LabelTransform method) (cellmil.datamodels.transforms.LabelTransformPipeline method) (cellmil.datamodels.transforms.normalization.RobustScalerTransform method) (cellmil.datamodels.transforms.pipeline.TransformPipeline method) (cellmil.datamodels.transforms.RobustScalerTransform method) (cellmil.datamodels.transforms.time_discretizer.TimeDiscretizerTransform method) (cellmil.datamodels.transforms.TimeDiscretizerTransform method) (cellmil.datamodels.transforms.Transform method) (cellmil.datamodels.transforms.TransformPipeline method) get_config_for_hashing() (cellmil.datamodels.transforms.pipeline.TransformPipeline method) (cellmil.datamodels.transforms.TransformPipeline method) get_constant_features_mask() (cellmil.datamodels.transforms.normalization.RobustScalerTransform method) (cellmil.datamodels.transforms.RobustScalerTransform method) get_correlation_mask() (cellmil.datamodels.datasets.neoplastic_dataset.NeoplasticDataset method) (cellmil.datamodels.datasets.NeoplasticDataset method) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset method) (cellmil.datamodels.datasets.patch_mil_dataset.PatchMILDataset method) get_cpu_count() (in module cellmil.utils.tools) get_edge_patch() (in module cellmil.segmentation.cell_segmenter) get_experiment_id() (cellmil.utils.wandb.WandbClient method) get_experiment_summary() (cellmil.datamodels.model.ModelStorage method) get_feature_importance_mask() (cellmil.datamodels.transforms.correlation_filter.CorrelationFilterTransform method) (cellmil.datamodels.transforms.CorrelationFilterTransform method) get_feature_path() (in module cellmil.datamodels.datasets.utils) get_features() (cellmil.features.feature_extractor.FeatureExtractor method) (cellmil.features.FeatureExtractor method) get_fold_indices() (cellmil.datamodels.model.ModelStorage method) get_he_ref() (cellmil.utils.stain_normalization.NormalizeParameters method) get_hyperparameters() (cellmil.models.mil.graphmil.GlobalPooling_Classifier method) (cellmil.models.mil.graphmil.GNN method) (cellmil.models.mil.graphmil.gnn.GNN method) (cellmil.models.mil.graphmil.pool.GlobalPooling_Classifier method) get_instance_gradients() (cellmil.models.mil.histobistro.HistoBistro method) get_max_sat() (cellmil.utils.stain_normalization.NormalizeParameters method) get_metric() (cellmil.utils.wandb.WandbClient static method) get_negative_entropy() (cellmil.models.mil.utils.AEM method) get_normalization_params() (cellmil.datamodels.datasets.neoplastic_dataset.NeoplasticDataset method) (cellmil.datamodels.datasets.NeoplasticDataset method) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset method) (cellmil.datamodels.datasets.patch_mil_dataset.PatchMILDataset method) get_normalized_gradients() (cellmil.models.mil.histobistro.HistoBistro method) get_num_classes() (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) get_num_labels() (cellmil.datamodels.datasets.cell_gnn_mil_dataset.CellGNNMILDataset method) (cellmil.datamodels.datasets.cell_gnn_mil_dataset.SubsetCellGNNMILDataset method) (cellmil.datamodels.datasets.cell_mil_dataset.CellMILDataset method) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset method) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.SubsetPatchGNNMILDataset method) (cellmil.datamodels.datasets.patch_mil_dataset.PatchMILDataset method) get_number_patches() (cellmil.datamodels.WSI method) (cellmil.datamodels.wsi.WSI method) get_patches() (cellmil.data.patch_extractor.PatchExtractor method) (cellmil.data.PatchExtractor method) (cellmil.datamodels.WSI method) (cellmil.datamodels.wsi.WSI method) get_removed_feature_indices() (cellmil.datamodels.transforms.correlation_filter.CorrelationFilterTransform method) (cellmil.datamodels.transforms.CorrelationFilterTransform method) get_runs() (cellmil.utils.wandb.WandbClient method) get_scaling_parameters() (cellmil.datamodels.transforms.normalization.RobustScalerTransform method) (cellmil.datamodels.transforms.RobustScalerTransform method) get_self_attention() (cellmil.models.mil.histobistro.Attention method) get_size_of_dict() (in module cellmil.utils.tools) get_summary() (cellmil.models.mil.utils.Accuracy_Logger method) get_task() (cellmil.utils.wandb.WandbClient method) get_template_point() (in module cellmil.utils.templates) get_template_segmentation() (in module cellmil.utils.templates) get_tile() (cellmil.data.cucim_deepzoom.DeepZoomGeneratorCucim method) get_train_val_dataloaders() (cellmil.utils.train.evals.k_fold_cross_validation.KFoldCrossValidation method) (cellmil.utils.train.evals.KFoldCrossValidation method) get_weight() (cellmil.models.mil.utils.AEM method) get_weights_for_sampler() (cellmil.datamodels.datasets.cell_mil_dataset.CellMILDataset method) (cellmil.datamodels.datasets.celltype_dataset.CellTypeDataset method) (cellmil.datamodels.datasets.CellTypeDataset method) (cellmil.datamodels.datasets.neoplastic_dataset.NeoplasticDataset method) (cellmil.datamodels.datasets.NeoplasticDataset method) (cellmil.datamodels.datasets.patch_mil_dataset.PatchMILDataset method) gigapath command line option GigapathExtractor (class in cellmil.features.extractor.embedding) GlobalPooling_Classifier (class in cellmil.models.mil.graphmil) (class in cellmil.models.mil.graphmil.pool) GNN (class in cellmil.models.mil.graphmil) (class in cellmil.models.mil.graphmil.gnn) GNN_KEY (cellmil.statistics.stats_printer.StatsPrinter attribute) (cellmil.statistics.StatsPrinter attribute) gnn_layer (cellmil.interfaces.AttentionExplainerConfig.Aggregation attribute) gnn_layer_index (cellmil.interfaces.AttentionExplainerConfig.AttentionExplainerConfig attribute) gnn_mil (cellmil.interfaces.MIL.RouteType attribute) gnn_only (cellmil.interfaces.AttentionExplainerConfig.Aggregation attribute) GNNMILDataset() (in module cellmil.datamodels.datasets) (in module cellmil.datamodels.datasets.gnn_mil_dataset) GNNS_KEY (cellmil.statistics.stats_printer.StatsPrinter attribute) (cellmil.statistics.StatsPrinter attribute) gpu (cellmil.interfaces.CellSegmenterConfig attribute), [1] (cellmil.interfaces.DatasetCreatorConfig attribute), [1] (cellmil.interfaces.GraphCreatorConfig attribute), [1] (cellmil.interfaces.MILPredictorConfig attribute), [1] (cellmil.interfaces.MILTrainerConfig attribute), [1] gpu: command line option gradient (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerType attribute) graph (cellmil.interfaces.AttentionExplainerConfig.VisualizationMode attribute) graph_creation() (in module cellmil.cli.graph_creation) graph_creator (cellmil.interfaces.MILTrainerConfig attribute), [1] graph_method (cellmil.interfaces.FeatureExtractorConfig attribute), [1] graph_methods (cellmil.interfaces.DatasetCreatorConfig attribute), [1] GraphCreator (class in cellmil.graph) (class in cellmil.graph.graph_creator) GraphCreatorConfig (class in cellmil.interfaces), [1] GraphCreatorConfig.Config (class in cellmil.interfaces), [1] GraphDebugVisualizer (class in cellmil.graph.debug_visualizer) graphmil (cellmil.interfaces.MIL.MILType attribute) group_centroids_by_type() (in module cellmil.models.segmentation.hovernet) H has_final_model() (cellmil.datamodels.model.ModelStorage method) has_regularization (cellmil.utils.wandb.ExperimentComponents property) has_stratification (cellmil.utils.wandb.ExperimentComponents property) head4type (cellmil.interfaces.MIL.MILType attribute) Head4Type (class in cellmil.models.mil.head4type) higher_is_better (cellmil.utils.train.metrics.BrierScore attribute) (cellmil.utils.train.metrics.ConcordanceIndex attribute) histobistro (cellmil.interfaces.MIL.MILType attribute) HistoBistro (class in cellmil.models.mil.histobistro) HoVerNet (class in cellmil.models.segmentation) (class in cellmil.models.segmentation.hovernet) I include_non_regularized (cellmil.interfaces.TableConfig.TableConfig attribute) include_regularized (cellmil.interfaces.TableConfig.TableConfig attribute) include_stratified (cellmil.interfaces.TableConfig.TableConfig attribute) init_vit_b() (cellmil.models.segmentation.cellvit.CellViTSAM method) (cellmil.models.segmentation.CellViTSAM method) init_vit_h() (cellmil.models.segmentation.cellvit.CellViTSAM method) (cellmil.models.segmentation.CellViTSAM method) init_vit_l() (cellmil.models.segmentation.cellvit.CellViTSAM method) (cellmil.models.segmentation.CellViTSAM method) initialize() (cellmil.models.mil.utils.Accuracy_Logger method) inst_eval() (cellmil.models.mil.clam.CLAM_SB method) inst_eval_out() (cellmil.models.mil.clam.CLAM_SB method) is_differentiable (cellmil.utils.train.metrics.BrierScore attribute) (cellmil.utils.train.metrics.ConcordanceIndex attribute) is_survival (cellmil.datamodels.model.ExperimentMetadata attribute) (cellmil.datamodels.model.FoldMetadata attribute) is_survival_model() (in module cellmil.utils.train.evals.utils) K k (cellmil.graph.creator.EdgeCreator attribute) k_folds (cellmil.datamodels.model.ExperimentMetadata attribute) kernel (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerType attribute) KFoldCrossValidation (class in cellmil.utils.train.evals) (class in cellmil.utils.train.evals.k_fold_cross_validation) KNNEdgeCreator (class in cellmil.graph.creator) L label (cellmil.datamodels.WSI attribute) (cellmil.datamodels.wsi.WSI attribute) (cellmil.interfaces.MILTrainerConfig attribute), [1] (cellmil.interfaces.TableConfig.TableConfig attribute) LabelTransform (class in cellmil.datamodels.transforms) (class in cellmil.datamodels.transforms.base_label_transform) LabelTransformPipeline (class in cellmil.datamodels.transforms) (class in cellmil.datamodels.transforms.label_pipeline) limit_radius (cellmil.graph.creator.EdgeCreator attribute) list_folds() (cellmil.datamodels.model.ModelStorage method) LitAttentionDeepMIL (class in cellmil.models.mil) (class in cellmil.models.mil.attentiondeepmil) LitCellConv (class in cellmil.models.mil.cellconv) LitCLAM (class in cellmil.models.mil) (class in cellmil.models.mil.clam) LitGeneral (class in cellmil.models.mil.utils) LitGraphMIL (class in cellmil.models.mil) (class in cellmil.models.mil.graphmil) LitHead4Type (class in cellmil.models.mil.head4type) LitMultiFocus (class in cellmil.models.mil.multifocus) LitStandard (class in cellmil.models.mil) (class in cellmil.models.mil.standard) LitSurvAttentionDeepMIL (class in cellmil.models.mil.attentiondeepmil) LitSurvCellConv (class in cellmil.models.mil.cellconv) LitSurvCLAM (class in cellmil.models.mil.clam) LitSurvGraphMIL (class in cellmil.models.mil.graphmil) LitSurvHead4Type (class in cellmil.models.mil.head4type) load() (cellmil.datamodels.transforms.base_label_transform.LabelTransform class method) (cellmil.datamodels.transforms.base_transform.Transform class method) (cellmil.datamodels.transforms.label_pipeline.LabelTransformPipeline class method) (cellmil.datamodels.transforms.LabelTransform class method) (cellmil.datamodels.transforms.LabelTransformPipeline class method) (cellmil.datamodels.transforms.pipeline.TransformPipeline class method) (cellmil.datamodels.transforms.time_discretizer.TimeDiscretizerTransform class method) (cellmil.datamodels.transforms.TimeDiscretizerTransform class method) (cellmil.datamodels.transforms.Transform class method) (cellmil.datamodels.transforms.TransformPipeline class method) load_all_predictions() (cellmil.datamodels.model.ModelStorage method) load_embedding() (cellmil.datamodels.WSI method) (cellmil.datamodels.wsi.WSI method) load_final_checkpoint() (cellmil.datamodels.model.ModelStorage method) load_final_transforms() (cellmil.datamodels.model.ModelStorage method) load_fold_checkpoint() (cellmil.datamodels.model.ModelStorage method) load_fold_predictions() (cellmil.datamodels.model.ModelStorage method) load_fold_transforms() (cellmil.datamodels.model.ModelStorage method) load_from_checkpoint() (cellmil.models.mil.attentiondeepmil.LitAttentionDeepMIL class method) (cellmil.models.mil.cellconv.LitCellConv class method) (cellmil.models.mil.clam.LitCLAM class method) (cellmil.models.mil.graphmil.LitGraphMIL class method) (cellmil.models.mil.head4type.LitHead4Type class method) (cellmil.models.mil.LitAttentionDeepMIL class method) (cellmil.models.mil.LitCLAM class method) (cellmil.models.mil.LitGraphMIL class method) (cellmil.models.mil.multifocus.LitMultiFocus class method) load_patch_metadata() (cellmil.datamodels.WSI method) (cellmil.datamodels.wsi.WSI method) load_precomputed_graph() (in module cellmil.datamodels.datasets.utils) load_pretrained_encoder() (cellmil.models.segmentation.cellvit.CellViTSAM method) (cellmil.models.segmentation.CellViTSAM method) load_roi_for_slide() (in module cellmil.datamodels.datasets.utils) load_state_dict() (cellmil.models.segmentation.cellpose.CellposeSAM method) log() (cellmil.models.mil.utils.Accuracy_Logger method) log_batch() (cellmil.models.mil.utils.Accuracy_Logger method) logger (cellmil.datamodels.WSI attribute) (cellmil.datamodels.wsi.WSI attribute) loss_hovernet() (in module cellmil.models.segmentation.hovernet) M macenko_normalization() (in module cellmil.utils.stain_normalization) main() (in module cellmil.cli.cell_segmentation) (in module cellmil.cli.dataset_creation) (in module cellmil.cli.eval_external) (in module cellmil.cli.eval_report) (in module cellmil.cli.feature_extraction) (in module cellmil.cli.graph_creation) (in module cellmil.cli.patch_extraction) (in module cellmil.cli.stats_print) (in module cellmil.cli.visualize_features) majority (cellmil.interfaces.EvaluationExternalValidatorConfig.AggregationMethod attribute) max_total_samples (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig attribute) mean (cellmil.interfaces.EvaluationExternalValidatorConfig.AggregationMethod attribute) Mean_MLP (class in cellmil.models.mil.graphmil) (class in cellmil.models.mil.graphmil.pool) median (cellmil.interfaces.EvaluationExternalValidatorConfig.AggregationMethod attribute) merge_graph_with_features() (in module cellmil.datamodels.datasets.utils) metadata (cellmil.datamodels.WSI attribute) (cellmil.datamodels.wsi.WSI attribute) method command line option method (cellmil.interfaces.GraphCreatorConfig attribute), [1] metric_mapping (cellmil.interfaces.TableConfig.TableConfig attribute) metric_name (cellmil.datamodels.model.FoldMetadata attribute) metrics (cellmil.datamodels.model.FoldMetadata attribute) (cellmil.interfaces.EvaluationExternalValidatorConfig.EvaluationExternalValidatorConfig attribute) (cellmil.interfaces.EvaluationReporterConfig.EvaluationReporterConfig attribute) METRICS (cellmil.statistics.stats_printer.StatsPrinter attribute) (cellmil.statistics.StatsPrinter attribute) Metrics (class in cellmil.interfaces.EvaluationReporterConfig) mil (cellmil.interfaces.MIL.RouteType attribute) MIL_fc (class in cellmil.models.mil.standard) MIL_fc_mc (class in cellmil.models.mil.standard) MIL_KEY (cellmil.statistics.stats_printer.StatsPrinter attribute) (cellmil.statistics.StatsPrinter attribute) MILDataset() (in module cellmil.datamodels.datasets) (in module cellmil.datamodels.datasets.mil_dataset) MILPredictorConfig (class in cellmil.interfaces), [1] MILPredictorConfig.Config (class in cellmil.interfaces), [1] MILS_KEY (cellmil.statistics.stats_printer.StatsPrinter attribute) (cellmil.statistics.StatsPrinter attribute) MILTrainerConfig (class in cellmil.interfaces), [1] MILTrainerConfig.Config (class in cellmil.interfaces), [1] MILType (class in cellmil.interfaces.MIL) min_max (cellmil.interfaces.AttentionExplainerConfig.Normalization attribute) model (cellmil.interfaces.CellSegmenterConfig attribute), [1] (cellmil.interfaces.MILPredictorConfig attribute), [1] (cellmil.interfaces.MILTrainerConfig attribute), [1] (cellmil.utils.wandb.ExperimentComponents attribute) model_config (cellmil.datamodels.model.ExperimentMetadata attribute) (cellmil.interfaces.AttentionExplainerConfig.AttentionExplainerConfig attribute) (cellmil.interfaces.CellSegmenterConfig attribute), [1] (cellmil.interfaces.DatasetCreatorConfig attribute), [1] (cellmil.interfaces.EvaluationExternalValidatorConfig.EvaluationExternalValidatorConfig attribute) (cellmil.interfaces.EvaluationReporterConfig.EvaluationReporterConfig attribute) (cellmil.interfaces.FeatureExtractorConfig attribute), [1] (cellmil.interfaces.FeatureVisualizerConfig attribute), [1] (cellmil.interfaces.GraphCreatorConfig attribute), [1] (cellmil.interfaces.MILPredictorConfig attribute), [1] (cellmil.interfaces.MILTrainerConfig attribute), [1] (cellmil.interfaces.PatchExtractorConfig attribute), [1] (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig attribute) (cellmil.interfaces.StatsPrinterConfig.StatsPrinterConfig attribute) model_mapping (cellmil.interfaces.TableConfig.TableConfig attribute) models (cellmil.interfaces.TableConfig.TableConfig attribute) models_dir (cellmil.interfaces.EvaluationExternalValidatorConfig.EvaluationExternalValidatorConfig attribute) ModelStorage (class in cellmil.datamodels.model) module cellmil.cli cellmil.cli.cell_segmentation cellmil.cli.dataset_creation cellmil.cli.eval_external cellmil.cli.eval_report cellmil.cli.feature_extraction cellmil.cli.graph_creation cellmil.cli.patch_extraction cellmil.cli.stats_print cellmil.cli.visualize_features cellmil.config.python cellmil.config.python.config cellmil.data cellmil.data.cucim_deepzoom cellmil.data.patch_extractor cellmil.data.storage cellmil.datamodels cellmil.datamodels.datasets cellmil.datamodels.datasets.cell_gnn_mil_dataset cellmil.datamodels.datasets.cell_mil_dataset cellmil.datamodels.datasets.celltype_dataset cellmil.datamodels.datasets.gnn_mil_dataset cellmil.datamodels.datasets.mil_dataset cellmil.datamodels.datasets.neoplastic_dataset cellmil.datamodels.datasets.patch_gnn_mil_dataset cellmil.datamodels.datasets.patch_mil_dataset cellmil.datamodels.datasets.utils cellmil.datamodels.model cellmil.datamodels.transforms cellmil.datamodels.transforms.base_label_transform cellmil.datamodels.transforms.base_transform cellmil.datamodels.transforms.correlation_filter cellmil.datamodels.transforms.label_pipeline cellmil.datamodels.transforms.normalization cellmil.datamodels.transforms.pipeline cellmil.datamodels.transforms.time_discretizer cellmil.datamodels.wsi cellmil.dataset cellmil.dataset.dataset_creator cellmil.features cellmil.features.extractor cellmil.features.extractor.embedding cellmil.features.extractor.morphological cellmil.features.extractor.topological cellmil.features.feature_extractor cellmil.graph cellmil.graph.creator cellmil.graph.debug_visualizer cellmil.graph.graph_creator cellmil.interfaces cellmil.interfaces.AttentionExplainerConfig cellmil.interfaces.EvaluationExternalValidatorConfig cellmil.interfaces.EvaluationReporterConfig cellmil.interfaces.MIL cellmil.interfaces.SHAPExplainerConfig cellmil.interfaces.StatsPrinterConfig cellmil.interfaces.TableConfig cellmil.models cellmil.models.mil cellmil.models.mil.attentiondeepmil cellmil.models.mil.cellconv cellmil.models.mil.clam cellmil.models.mil.graphmil cellmil.models.mil.graphmil.gnn cellmil.models.mil.graphmil.pool cellmil.models.mil.head4type cellmil.models.mil.histobistro cellmil.models.mil.multifocus cellmil.models.mil.standard cellmil.models.mil.transmil cellmil.models.mil.utils cellmil.models.segmentation cellmil.models.segmentation.cellpose cellmil.models.segmentation.cellposeV2 cellmil.models.segmentation.cellvit cellmil.models.segmentation.hovernet cellmil.segmentation cellmil.segmentation.cell_segmenter cellmil.statistics cellmil.statistics.stats_printer cellmil.utils cellmil.utils.dataset_from_dataset cellmil.utils.stain_normalization cellmil.utils.templates cellmil.utils.tools cellmil.utils.train cellmil.utils.train.callbacks cellmil.utils.train.dataset cellmil.utils.train.evals cellmil.utils.train.evals.k_fold_cross_validation cellmil.utils.train.evals.utils cellmil.utils.train.losses cellmil.utils.train.metrics cellmil.utils.wandb cellmil.visualization cellmil.visualization.feature_visualizer module_exists() (in module cellmil.utils.tools) MorphologicalExtractor (class in cellmil.features.extractor.morphological) morphometrics command line option MorphometricsExtractor (class in cellmil.features.extractor.morphological) multifocus (cellmil.interfaces.MIL.MILType attribute) MultiFocus (class in cellmil.models.mil.multifocus) N n_bins (cellmil.interfaces.MILTrainerConfig attribute), [1] name (cellmil.datamodels.model.ExperimentMetadata attribute) (cellmil.datamodels.WSI attribute) (cellmil.datamodels.wsi.WSI attribute) NegativeLogLikelihoodSurvLoss (class in cellmil.utils.train.losses) NeoplasticDataset (class in cellmil.datamodels.datasets) (class in cellmil.datamodels.datasets.neoplastic_dataset) none (cellmil.interfaces.AttentionExplainerConfig.Normalization attribute) normalization (cellmil.interfaces.AttentionExplainerConfig.AttentionExplainerConfig attribute) (cellmil.interfaces.MILTrainerConfig attribute), [1] Normalization (class in cellmil.interfaces.AttentionExplainerConfig) normalize_attention (cellmil.interfaces.AttentionExplainerConfig.AttentionExplainerConfig attribute) NormalizeParameters (class in cellmil.utils.stain_normalization) nsamples (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig attribute) num_bins (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig attribute) num_classes (cellmil.datamodels.datasets.cell_gnn_mil_dataset.SubsetCellGNNMILDataset property) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.SubsetPatchGNNMILDataset property) O on_before_batch_transfer() (cellmil.models.mil.graphmil.LitGraphMIL method) (cellmil.models.mil.LitGraphMIL method) on_test_epoch_end() (cellmil.models.mil.clam.LitCLAM method) (cellmil.models.mil.graphmil.LitGraphMIL method) (cellmil.models.mil.LitCLAM method) (cellmil.models.mil.LitGraphMIL method) on_train_epoch_end() (cellmil.models.mil.clam.LitCLAM method) (cellmil.models.mil.graphmil.LitGraphMIL method) (cellmil.models.mil.LitCLAM method) (cellmil.models.mil.LitGraphMIL method) (cellmil.models.mil.utils.LitGeneral method) on_validation_epoch_end() (cellmil.models.mil.clam.LitCLAM method) (cellmil.models.mil.graphmil.LitGraphMIL method) (cellmil.models.mil.LitCLAM method) (cellmil.models.mil.LitGraphMIL method) (cellmil.models.mil.utils.LitGeneral method) ours (cellmil.interfaces.MIL.MILType attribute) output_dir (cellmil.interfaces.EvaluationExternalValidatorConfig.EvaluationExternalValidatorConfig attribute) (cellmil.interfaces.EvaluationReporterConfig.EvaluationReporterConfig attribute) output_file (cellmil.interfaces.TableConfig.TableConfig attribute) output_path (cellmil.interfaces.AttentionExplainerConfig.AttentionExplainerConfig attribute) (cellmil.interfaces.DatasetCreatorConfig attribute), [1] (cellmil.interfaces.PatchExtractorConfig attribute), [1] (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig attribute) P parameters() (cellmil.models.segmentation.cellpose.CellposeSAM method) parse_experiment_components() (cellmil.utils.wandb.WandbClient static method) patch_extraction() (in module cellmil.cli.patch_extraction) patch_overlap (cellmil.interfaces.PatchExtractorConfig attribute), [1] patch_size (cellmil.interfaces.PatchExtractorConfig attribute), [1] patch_transform (cellmil.datamodels.WSI attribute) (cellmil.datamodels.wsi.WSI attribute) patched_slide_path command line option patched_slide_path (cellmil.datamodels.WSI attribute) (cellmil.datamodels.wsi.WSI attribute) (cellmil.interfaces.CellSegmenterConfig attribute), [1] (cellmil.interfaces.FeatureExtractorConfig attribute), [1] (cellmil.interfaces.GraphCreatorConfig attribute), [1] (cellmil.interfaces.MILPredictorConfig attribute), [1] patches_list (cellmil.datamodels.WSI attribute) (cellmil.datamodels.wsi.WSI attribute) PatchExtractor (class in cellmil.data) (class in cellmil.data.patch_extractor) PatchExtractorConfig (class in cellmil.interfaces), [1] PatchExtractorConfig.Config (class in cellmil.interfaces), [1] PatchGNNMILDataset (class in cellmil.datamodels.datasets.patch_gnn_mil_dataset) PatchMILDataset (class in cellmil.datamodels.datasets.patch_mil_dataset) patient (cellmil.datamodels.WSI attribute) (cellmil.datamodels.wsi.WSI attribute) plot command line option plot (cellmil.interfaces.GraphCreatorConfig attribute), [1] plot_graph() (in module cellmil.utils.tools) plot_vector() (in module cellmil.utils.tools) pooling_only (cellmil.interfaces.AttentionExplainerConfig.Aggregation attribute) post_process_batch_hovernet() (in module cellmil.models.segmentation.hovernet) post_process_cells() (cellmil.segmentation.cell_segmenter.CellPostProcessor method) post_process_edge_cells() (cellmil.segmentation.cell_segmenter.CellSegmenter method) (cellmil.segmentation.CellSegmenter method) PPEG (class in cellmil.models.mil.transmil) precision (cellmil.interfaces.EvaluationReporterConfig.Metrics attribute) (cellmil.interfaces.TableConfig.TableConfig attribute) predict_step() (cellmil.models.mil.attentiondeepmil.LitSurvAttentionDeepMIL method) (cellmil.models.mil.cellconv.LitSurvCellConv method) (cellmil.models.mil.clam.LitCLAM method) (cellmil.models.mil.clam.LitSurvCLAM method) (cellmil.models.mil.graphmil.LitGraphMIL method) (cellmil.models.mil.graphmil.LitSurvGraphMIL method) (cellmil.models.mil.head4type.LitSurvHead4Type method) (cellmil.models.mil.LitCLAM method) (cellmil.models.mil.LitGraphMIL method) (cellmil.models.mil.utils.LitGeneral method) PreNorm (class in cellmil.models.mil.histobistro) preprocess_row() (in module cellmil.datamodels.datasets.utils) process() (cellmil.datamodels.datasets.cell_gnn_mil_dataset.CellGNNMILDataset method) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset method) (cellmil.segmentation.cell_segmenter.CellSegmenter method) (cellmil.segmentation.CellSegmenter method) process_patch_image() (cellmil.datamodels.WSI method) (cellmil.datamodels.wsi.WSI method) process_queue() (cellmil.data.patch_extractor.PatchExtractor method) (cellmil.data.PatchExtractor method) processed_file_names (cellmil.datamodels.datasets.cell_gnn_mil_dataset.CellGNNMILDataset property) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset property) projects (cellmil.interfaces.EvaluationReporterConfig.EvaluationReporterConfig attribute) (cellmil.interfaces.StatsPrinterConfig.StatsPrinterConfig attribute) pyradiomics_hed command line option pyradiomics_hue command line option PyRadiomicsExtractor (class in cellmil.features.extractor.morphological) Q queue_worker() (in module cellmil.data.patch_extractor) R radius command line option radius (cellmil.graph.creator.EdgeCreator attribute) RadiusEdgeCreator (class in cellmil.graph.creator) random_seed (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig attribute) random_state (cellmil.datamodels.model.ExperimentMetadata attribute) random_walk (cellmil.interfaces.AttentionExplainerConfig.Aggregation attribute) raw_file_names (cellmil.datamodels.datasets.cell_gnn_mil_dataset.CellGNNMILDataset property) (cellmil.datamodels.datasets.patch_gnn_mil_dataset.PatchGNNMILDataset property) recall (cellmil.interfaces.EvaluationReporterConfig.Metrics attribute) regularization (cellmil.utils.wandb.ExperimentComponents attribute) remove_small_objs() (in module cellmil.models.segmentation.hovernet) remove_transform() (cellmil.datamodels.transforms.pipeline.TransformPipeline method) (cellmil.datamodels.transforms.TransformPipeline method) Report (class in cellmil.utils.train.evals.utils) reset_parameters() (cellmil.models.mil.graphmil.gnn.SGFormerAttention method) resnet50 command line option ResNet50Extractor (class in cellmil.features.extractor.embedding) RGB_to_OD() (in module cellmil.utils.stain_normalization) robust (cellmil.interfaces.AttentionExplainerConfig.Normalization attribute) RobustScalerTransform (class in cellmil.datamodels.transforms) (class in cellmil.datamodels.transforms.normalization) root (cellmil.interfaces.MILTrainerConfig attribute), [1] root_dir (cellmil.interfaces.EvaluationExternalValidatorConfig.EvaluationExternalValidatorConfig attribute) RouteType (class in cellmil.interfaces.MIL) run() (cellmil.graph.debug_visualizer.GraphDebugVisualizer method) run_configs (cellmil.statistics.stats_printer.StatsPrinter attribute) S SAGE (class in cellmil.models.mil.graphmil) (class in cellmil.models.mil.graphmil.gnn) samples_per_bin (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig attribute) save() (cellmil.datamodels.transforms.base_label_transform.LabelTransform method) (cellmil.datamodels.transforms.base_transform.Transform method) (cellmil.datamodels.transforms.label_pipeline.LabelTransformPipeline method) (cellmil.datamodels.transforms.LabelTransform method) (cellmil.datamodels.transforms.LabelTransformPipeline method) (cellmil.datamodels.transforms.pipeline.TransformPipeline method) (cellmil.datamodels.transforms.time_discretizer.TimeDiscretizerTransform method) (cellmil.datamodels.transforms.TimeDiscretizerTransform method) (cellmil.datamodels.transforms.Transform method) (cellmil.datamodels.transforms.TransformPipeline method) save_annotation_mask() (cellmil.data.storage.Storage method) save_attention_map() (cellmil.models.mil.histobistro.Attention method) save_attn_gradients() (cellmil.models.mil.histobistro.Attention method) save_checkpoint() (cellmil.models.mil.utils.EarlyStopping method) save_elem_to_disk() (cellmil.data.storage.Storage method) save_experiment_metadata() (cellmil.datamodels.model.ModelStorage method) save_final_model() (cellmil.datamodels.model.ModelStorage method) save_fold_results() (cellmil.datamodels.model.ModelStorage method) save_gradient() (cellmil.models.mil.histobistro.HistoBistro method) save_masks() (cellmil.data.storage.Storage method) save_meta_data() (cellmil.data.storage.Storage method) save_raw_shap_values (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig attribute) save_thumbnails() (cellmil.data.storage.Storage method) segmentation_model (cellmil.interfaces.FeatureExtractorConfig attribute), [1] (cellmil.interfaces.GraphCreatorConfig attribute), [1] (cellmil.interfaces.MILPredictorConfig attribute), [1] (cellmil.interfaces.MILTrainerConfig attribute), [1] segmentation_models (cellmil.interfaces.DatasetCreatorConfig attribute), [1] set_patch_transform() (cellmil.datamodels.WSI method) (cellmil.datamodels.wsi.WSI method) set_wsi() (cellmil.segmentation.cell_segmenter.CellSegmenter method) (cellmil.segmentation.CellSegmenter method) setup_output_path() (cellmil.data.patch_extractor.PatchExtractor static method) (cellmil.data.PatchExtractor static method) setup_parser() (in module cellmil.cli.cell_segmentation) (in module cellmil.cli.dataset_creation) (in module cellmil.cli.eval_external) (in module cellmil.cli.eval_report) (in module cellmil.cli.feature_extraction) (in module cellmil.cli.graph_creation) (in module cellmil.cli.patch_extraction) (in module cellmil.cli.stats_print) (in module cellmil.cli.visualize_features) SGFormer (class in cellmil.models.mil.graphmil) (class in cellmil.models.mil.graphmil.gnn) SGFormerAttention (class in cellmil.models.mil.graphmil.gnn) SHAPExplainerConfig (class in cellmil.interfaces.SHAPExplainerConfig) SHAPExplainerType (class in cellmil.interfaces.SHAPExplainerConfig) sigmoid (cellmil.interfaces.AttentionExplainerConfig.Normalization attribute) SimilarityEdgeCreator (class in cellmil.graph.creator) slide_path (cellmil.datamodels.WSI attribute) (cellmil.datamodels.wsi.WSI attribute) SmallWorld (class in cellmil.models.mil.graphmil) (class in cellmil.models.mil.graphmil.gnn) softmax (cellmil.interfaces.AttentionExplainerConfig.Normalization attribute) split_dataset() (in module cellmil.utils.train) (in module cellmil.utils.train.dataset) standard (cellmil.interfaces.MIL.MILType attribute) Standard (class in cellmil.models.mil.graphmil) (class in cellmil.models.mil.graphmil.pool) start_timer() (in module cellmil.utils.tools) state_dict() (cellmil.models.segmentation.cellpose.CellposeSAM method) stats_print() (in module cellmil.cli.stats_print) StatsPrinter (class in cellmil.statistics) (class in cellmil.statistics.stats_printer) StatsPrinterConfig (class in cellmil.interfaces.StatsPrinterConfig) StatsPrinterConfig.Config (class in cellmil.interfaces.StatsPrinterConfig) Storage (class in cellmil.data.storage) stratification (cellmil.utils.wandb.ExperimentComponents attribute) StructureExtractor (class in cellmil.features.extractor.topological) subsample_and_pad() (in module cellmil.datamodels.datasets.utils) SubsetCellGNNMILDataset (class in cellmil.datamodels.datasets.cell_gnn_mil_dataset) SubsetPatchGNNMILDataset (class in cellmil.datamodels.datasets.patch_gnn_mil_dataset) support_mapping (cellmil.interfaces.TableConfig.TableConfig attribute) survival_metrics (cellmil.interfaces.TableConfig.TableConfig attribute) T table_type (cellmil.interfaces.TableConfig.TableConfig attribute) TableConfig (class in cellmil.interfaces.TableConfig) target_mag (cellmil.interfaces.PatchExtractorConfig attribute), [1] task (cellmil.utils.wandb.ExperimentComponents attribute) task_mapping (cellmil.interfaces.TableConfig.TableConfig attribute) tasks (cellmil.interfaces.TableConfig.TableConfig attribute) (cellmil.statistics.stats_printer.StatsPrinter attribute) team (cellmil.interfaces.EvaluationReporterConfig.EvaluationReporterConfig attribute) (cellmil.interfaces.StatsPrinterConfig.StatsPrinterConfig attribute) test_step() (cellmil.models.mil.clam.LitCLAM method) (cellmil.models.mil.graphmil.LitGraphMIL method) (cellmil.models.mil.LitCLAM method) (cellmil.models.mil.LitGraphMIL method) TimeDiscretizerTransform (class in cellmil.datamodels.transforms) (class in cellmil.datamodels.transforms.time_discretizer) to() (cellmil.models.segmentation.cellpose.CellposeSAM method) (cellmil.models.segmentation.CellposeSAM method) (cellmil.models.segmentation.cellposeV2.CellposeSAM method) to_float() (in module cellmil.utils.tools) to_float_normalized() (in module cellmil.utils.tools) top_features (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig attribute) TopologicalExtractor (class in cellmil.features.extractor.topological) train() (cellmil.models.segmentation.cellpose.CellposeSAM method) (cellmil.models.segmentation.CellposeSAM method) (cellmil.models.segmentation.cellposeV2.CellposeSAM method) train_size (cellmil.datamodels.model.FoldMetadata attribute) training_step() (cellmil.models.mil.clam.LitCLAM method) (cellmil.models.mil.graphmil.LitGraphMIL method) (cellmil.models.mil.LitCLAM method) (cellmil.models.mil.LitGraphMIL method) (cellmil.models.mil.utils.LitGeneral method) transfer_batch_to_device() (cellmil.models.mil.cellconv.LitCellConv method) Transform (class in cellmil.datamodels.transforms) (class in cellmil.datamodels.transforms.base_transform) transform() (cellmil.datamodels.transforms.base_transform.FittableTransform method) (cellmil.datamodels.transforms.base_transform.Transform method) (cellmil.datamodels.transforms.FittableTransform method) (cellmil.datamodels.transforms.pipeline.TransformPipeline method) (cellmil.datamodels.transforms.Transform method) (cellmil.datamodels.transforms.TransformPipeline method) transform_labels() (cellmil.datamodels.transforms.base_label_transform.FittableLabelTransform method) (cellmil.datamodels.transforms.base_label_transform.LabelTransform method) (cellmil.datamodels.transforms.FittableLabelTransform method) (cellmil.datamodels.transforms.label_pipeline.LabelTransformPipeline method) (cellmil.datamodels.transforms.LabelTransform method) (cellmil.datamodels.transforms.LabelTransformPipeline method) TransformerBlocks (class in cellmil.models.mil.histobistro) TransformPipeline (class in cellmil.datamodels.transforms) (class in cellmil.datamodels.transforms.pipeline) TransLayer (class in cellmil.models.mil.transmil) transmil (cellmil.interfaces.MIL.MILType attribute) TransMIL (class in cellmil.models.mil.transmil) U unflatten_dict() (in module cellmil.utils.tools) unfreeze_encoder() (cellmil.models.segmentation.cellvit.CellViT method) UNIExtractor (class in cellmil.features.extractor.embedding) uni} command line option update() (cellmil.utils.train.metrics.BrierScore method) (cellmil.utils.train.metrics.ConcordanceIndex method) V val_size (cellmil.datamodels.model.FoldMetadata attribute) validate_background_percentage() (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig class method) validate_extractors() (cellmil.interfaces.DatasetCreatorConfig class method), [1] validate_features() (in module cellmil.datamodels.datasets.utils) validate_gnn_layer_index() (cellmil.interfaces.AttentionExplainerConfig.AttentionExplainerConfig class method) validate_graph_methods() (cellmil.interfaces.DatasetCreatorConfig class method), [1] validate_model() (cellmil.interfaces.CellSegmenterConfig class method), [1] (cellmil.interfaces.FeatureExtractorConfig class method), [1] (cellmil.interfaces.GraphCreatorConfig class method), [1] (cellmil.interfaces.MILPredictorConfig class method), [1] (cellmil.interfaces.MILTrainerConfig class method), [1] validate_nsamples() (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig class method) validate_num_bins() (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig class method) validate_overlap() (cellmil.interfaces.PatchExtractorConfig class method), [1] validate_samples_per_bin() (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerConfig class method) validate_segmentation_model() (cellmil.interfaces.FeatureExtractorConfig class method), [1] (cellmil.interfaces.GraphCreatorConfig class method), [1] validate_segmentation_models() (cellmil.interfaces.DatasetCreatorConfig class method), [1] validation_step() (cellmil.models.mil.clam.LitCLAM method) (cellmil.models.mil.graphmil.LitGraphMIL method) (cellmil.models.mil.LitCLAM method) (cellmil.models.mil.LitGraphMIL method) (cellmil.models.mil.utils.LitGeneral method) values() (cellmil.interfaces.EvaluationExternalValidatorConfig.AggregationMethod class method) (cellmil.interfaces.EvaluationExternalValidatorConfig.FinalModel class method) (cellmil.interfaces.EvaluationReporterConfig.Metrics class method) (cellmil.interfaces.MIL.MILType class method) (cellmil.interfaces.SHAPExplainerConfig.SHAPExplainerType class method) visualization_mode (cellmil.interfaces.AttentionExplainerConfig.AttentionExplainerConfig attribute) VisualizationMode (class in cellmil.interfaces.AttentionExplainerConfig) visualize() (cellmil.visualization.feature_visualizer.FeatureVisualizer method) (cellmil.visualization.FeatureVisualizer method) visualize_cell_types (cellmil.interfaces.AttentionExplainerConfig.AttentionExplainerConfig attribute) visualize_features() (in module cellmil.cli.visualize_features) W WandbClient (class in cellmil.utils.wandb) weights_for_sampler() (in module cellmil.datamodels.datasets.utils) WSI (class in cellmil.datamodels) (class in cellmil.datamodels.wsi) wsi_path (cellmil.interfaces.CellSegmenterConfig attribute), [1] (cellmil.interfaces.FeatureExtractorConfig attribute), [1] (cellmil.interfaces.PatchExtractorConfig attribute), [1] wsl_preprocess() (in module cellmil.datamodels.datasets.utils) Z z_score (cellmil.interfaces.AttentionExplainerConfig.Normalization attribute)
