Index _ | A | B | C | D | E | F | G | H | I | J | L | M | N | P | Q | R | S | T | U | V | W | Y _ __init__() (slideflow.Dataset method) (slideflow.Heatmap method) (slideflow.io.torch.InterleaveIterator method) (slideflow.model.CPHTrainer method) (slideflow.model.DatasetFeatures method) (slideflow.model.Features method) (slideflow.model.LinearTrainer method) (slideflow.model.ModelParams method) (slideflow.model.Trainer method) (slideflow.Mosaic method) (slideflow.Project method) (slideflow.slide.TMA method) (slideflow.slide.WSI method) (slideflow.SlideMap method) (slideflow.util.ProgressBar method) (slideflow.util.TqdmLoggingHandler method) A activations_by_category() (slideflow.model.DatasetFeatures method) add_source() (slideflow.Project method) annotations (slideflow.Project property) associate_slide_names() (slideflow.Project method) B balance() (slideflow.Dataset method) basic_metrics() (in module slideflow.stats) box_plots() (slideflow.model.DatasetFeatures method) build_generator() (slideflow.slide.TMA method) (slideflow.slide.WSI method) build_index() (slideflow.Dataset method) build_model() (slideflow.model.ModelParams method) C calculate_centroid() (in module slideflow.stats) checkpoint_to_tf_model() (in module slideflow.io.tensorflow) choice_input() (in module slideflow.util) clear_filters() (slideflow.Dataset method) clip() (slideflow.Dataset method) cluster() (slideflow.SlideMap method) concordance_index() (in module slideflow.stats) CPHTrainer (class in slideflow.model) create_blank_annotations() (slideflow.Project method) create_hp_sweep() (slideflow.Project method) D Dataset (class in slideflow) dataset() (slideflow.Project method) dataset_config (slideflow.Project property) DatasetFeatures (class in slideflow.model) detect_tfrecord_format() (in module slideflow.io.tensorflow) (in module slideflow.io.torch) E emit() (slideflow.util.TqdmLoggingHandler method) eval_dir (slideflow.Project property) evaluate() (slideflow.model.CPHTrainer method) (slideflow.model.LinearTrainer method) (slideflow.model.Trainer method) (slideflow.Project method) evaluate_clam() (slideflow.Project method) export_to_csv() (slideflow.model.DatasetFeatures method) (slideflow.SlideMap method) export_to_torch() (slideflow.model.DatasetFeatures method) extract_tiles() (slideflow.Dataset method) (slideflow.Project method) (slideflow.slide.TMA method) (slideflow.slide.WSI method) extract_tiles_from_tfrecords() (slideflow.Dataset method) F Features (class in slideflow.model) FileFormatter (class in slideflow.util) filter() (slideflow.Dataset method) (slideflow.SlideMap method) filter_blank (slideflow.Dataset property) filtered_prediction() (in module slideflow.stats) filters (slideflow.Dataset property) float_input() (in module slideflow.util) focus() (slideflow.Mosaic method) format() (slideflow.util.FileFormatter method) (slideflow.util.LogFormatter method) from_features() (slideflow.SlideMap class method) from_model() (slideflow.model.Features class method) from_precalculated() (slideflow.SlideMap class method) from_prompt() (slideflow.Project class method) G gen_umap() (in module slideflow.stats) generate_combined_roc() (in module slideflow.stats) generate_features() (slideflow.Project method) generate_features_for_clam() (slideflow.Project method) generate_heatmaps() (slideflow.Project method) generate_mosaic() (slideflow.Project method) generate_mosaic_from_annotations() (slideflow.Project method) generate_roc() (in module slideflow.stats) generate_scatter() (in module slideflow.stats) generate_tfrecord_heatmap() (slideflow.Project method) generate_thumbnails() (slideflow.Project method) get_centroid_index() (in module slideflow.stats) get_label() (slideflow.io.torch.InterleaveIterator method) get_model_config() (in module slideflow.util) get_opt() (slideflow.model.ModelParams method) get_relative_tfrecord_paths() (in module slideflow.util) get_slide_paths() (in module slideflow.util) get_slides_from_model_manifest() (in module slideflow.util) get_tfrecord_parser() (in module slideflow.io.tensorflow) (in module slideflow.io.torch) get_tiles_in_area() (slideflow.SlideMap method) global_path() (in module slideflow.util) H harmonize_labels() (slideflow.Dataset method) Heatmap (class in slideflow) I int_input() (in module slideflow.util) interleave() (in module slideflow.io.tensorflow) (in module slideflow.io.torch) interleave_dataloader() (in module slideflow.io.torch) InterleaveIterator (class in slideflow.io.torch) is_float() (slideflow.Dataset method) J join_tfrecord() (in module slideflow.io.tensorflow) L label_by_logits() (slideflow.SlideMap method) label_by_meta() (slideflow.SlideMap method) label_by_slide() (slideflow.SlideMap method) label_by_uncertainty() (slideflow.SlideMap method) label_shape (slideflow.io.torch.InterleaveIterator property) labels() (slideflow.Dataset method) LinearTrainer (class in slideflow.model) load_cache() (slideflow.SlideMap method) load_csv_roi() (slideflow.slide.WSI method) load_indices() (slideflow.Dataset method) load_json() (in module slideflow.util) load_json_roi() (slideflow.slide.WSI method) load_project() (slideflow.Project method) loaded_correctly() (slideflow.slide.TMA method) (slideflow.slide.WSI method) LogFormatter (class in slideflow.util) logits_mean() (slideflow.model.DatasetFeatures method) logits_percent() (slideflow.model.DatasetFeatures method) logits_predict() (slideflow.model.DatasetFeatures method) M make_dir() (in module slideflow.util) manifest() (slideflow.Dataset method) map_to_predictions() (slideflow.model.DatasetFeatures method) merge() (slideflow.model.DatasetFeatures method) merge_split_tfrecords() (in module slideflow.io.tensorflow) metrics_from_dataset() (in module slideflow.stats) metrics_from_pred() (in module slideflow.stats) min_tiles (slideflow.Dataset property) model_type() (slideflow.model.ModelParams method) ModelParams (class in slideflow.model) models_dir (slideflow.Project property) module slideflow.io.tensorflow slideflow.io.torch slideflow.util Mosaic (class in slideflow) multi_image_example() (in module slideflow.io.tensorflow) multi_warn() (in module slideflow.util) N name (slideflow.Project property) neighbors() (slideflow.SlideMap method) neptune_api (slideflow.Project property) neptune_workspace (slideflow.Project property) normalize_layout() (in module slideflow.stats) num_tiles (slideflow.Dataset property) P parser_from_labels() (in module slideflow.io.tensorflow) path_input() (in module slideflow.util) path_to_ext() (in module slideflow.util) path_to_name() (in module slideflow.util) patients() (slideflow.Dataset method) permute_importance() (in module slideflow.stats) place_tiles() (slideflow.Mosaic method) pred_to_df() (in module slideflow.stats) predict() (slideflow.model.CPHTrainer method) (slideflow.model.LinearTrainer method) (slideflow.model.Trainer method) (slideflow.Project method) predict_from_layer() (in module slideflow.stats) predict_from_tensorflow() (in module slideflow.stats) predict_from_torch() (in module slideflow.stats) predict_wsi() (slideflow.Project method) preview() (slideflow.slide.TMA method) (slideflow.slide.WSI method) print_tfrecord() (in module slideflow.io.tensorflow) process_image() (in module slideflow.io.tensorflow) ProgressBar (class in slideflow.util) Project (class in slideflow) Q qc() (slideflow.slide.TMA method) (slideflow.slide.WSI method) R read_annotations() (in module slideflow.util) read_predictions() (in module slideflow.stats) reinforce_type() (slideflow.io.torch.InterleaveIterator method) relative_path() (in module slideflow.util) remove_filter() (slideflow.Dataset method) remove_slide() (slideflow.model.DatasetFeatures method) resize_tfrecords() (slideflow.Dataset method) rois() (slideflow.Dataset method) S save() (slideflow.Heatmap method) (slideflow.Mosaic method) (slideflow.Project method) (slideflow.SlideMap method) save_2d_plot() (slideflow.SlideMap method) save_3d_plot() (slideflow.SlideMap method) save_cache() (slideflow.SlideMap method) save_example_tiles() (slideflow.model.DatasetFeatures method) save_histogram() (in module slideflow.stats) save_report() (slideflow.Mosaic method) serialized_record() (in module slideflow.io.tensorflow) (in module slideflow.io.torch) show() (slideflow.Mosaic method) show_neighbors() (slideflow.SlideMap method) shuffle_tfrecord() (in module slideflow.io.tensorflow) shuffle_tfrecords_by_dir() (in module slideflow.io.tensorflow) slide_paths() (slideflow.Dataset method) slideflow.io.tensorflow module slideflow.io.torch module slideflow.util module SlideMap (class in slideflow) slides() (slideflow.Dataset method) sources (slideflow.Project property) split_tfrecord() (in module slideflow.io.tensorflow) split_tfrecords_by_roi() (slideflow.Dataset method) square_thumb() (slideflow.slide.TMA method) (slideflow.slide.WSI method) stats() (slideflow.model.DatasetFeatures method) T tensorflow() (slideflow.Dataset method) tfrecord_example() (in module slideflow.io.tensorflow) tfrecord_heatmap() (in module slideflow.util) tfrecord_report() (slideflow.Dataset method) tfrecords() (slideflow.Dataset method) tfrecords_by_subfolder() (slideflow.Dataset method) tfrecords_folders() (slideflow.Dataset method) tfrecords_from_tiles() (slideflow.Dataset method) thumb() (slideflow.slide.TMA method) (slideflow.slide.WSI method) TMA (class in slideflow.slide) to_onehot() (in module slideflow.stats) (in module slideflow.util) torch() (slideflow.Dataset method) TqdmLoggingHandler (class in slideflow.util) train() (slideflow.model.CPHTrainer method) (slideflow.model.LinearTrainer method) (slideflow.model.Trainer method) (slideflow.Project method) train_clam() (slideflow.Project method) train_val_split() (slideflow.Dataset method) Trainer (class in slideflow.model) trainer_from_hp() (in module slideflow.model) transform_tfrecord() (in module slideflow.io.tensorflow) U unclip() (slideflow.Dataset method) update_annotations_with_slidenames() (slideflow.Dataset method) update_manifest() (slideflow.Dataset method) update_results_log() (in module slideflow.util) update_tfrecord() (in module slideflow.io.tensorflow) update_tfrecord_dir() (in module slideflow.io.tensorflow) V validate() (slideflow.model.ModelParams method) verify_annotations_slides() (slideflow.Dataset method) W write_json() (in module slideflow.util) WSI (class in slideflow.slide) Y yes_no_input() (in module slideflow.util)