Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z _ __call__() (in module slideflow.model.Features) __init__() (ImgBatchSpeedColumn method) (LabeledMofNCompleteColumn method) (MultiprocessProgress method) (MultiprocessProgressTracker method) (SaliencyMap method) (Sidebar method) (Studio method) (StyleGAN2Interpolator method) A about() (in module slideflow) (in module slideflow.util) activations() (in module slideflow.SlideMap) activations_by_category() (in module slideflow.DatasetFeatures) add_inset() (in module slideflow.Heatmap) add_source() (in module slideflow.Project) add_to_render_pipeline() (Studio method) add_widgets() (Sidebar method) (Studio method) align_tiles_to() (in module slideflow.WSI) align_to() (in module slideflow.WSI) all() (SaliencyMap method) apply() (in module slideflow.biscuit.threshold) apply_qc_mask() (in module slideflow.WSI) apply_rois() (in module slideflow.cellseg.Segmentation) apply_segmentation() (in module slideflow.WSI) area() (in module slideflow.WSI) ask_load_heatmap() (Studio method) ask_load_model() (Studio method) ask_load_project() (Studio method) ask_load_slide() (Studio method) ask_zoom_to_mpp() (Studio method) associate_slide_names() (in module slideflow.Project) auc() (in module slideflow.biscuit.utils) auc_and_threshold() (in module slideflow.biscuit.utils) augment() (in module slideflow.norm.StainNormalizer) autoload() (Studio method) B balance() (in module slideflow.Dataset) batch() (in module slideflow.util) batch_generator() (in module slideflow.util) batched_predict() (in module slideflow.mil.MILModelConfig) (in module slideflow.mil.TrainerConfig) bin_values_to_slide_grid() (in module slideflow.util) blur_integrated_gradients() (SaliencyMap method) box_plots() (in module slideflow.DatasetFeatures) build_fastai_learner() (in module slideflow.mil) build_feature_extractor() (in module slideflow) (in module slideflow.model) build_generator() (in module slideflow.WSI) build_index() (in module slideflow.Dataset) build_model() (in module slideflow.mil.MILModelConfig) (in module slideflow.mil.TrainerConfig) build_mosaic() (in module slideflow.SlideMap) build_multimodal_learner() (in module slideflow.mil) build_train_dataloader() (in module slideflow.mil.TrainerConfig) build_trainer() (in module slideflow.model) build_val_dataloader() (in module slideflow.mil.TrainerConfig) C calculate_centroid() (in module slideflow.stats) calculate_centroids() (in module slideflow.cellseg.Segmentation) calculate_outlines() (in module slideflow.cellseg.Segmentation) cell_segmentation() (in module slideflow.Dataset) (in module slideflow.Project) center_next_window() (Studio method) centroid_to_image() (in module slideflow.cellseg.Segmentation) centroids() (in module slideflow.cellseg.Segmentation) check_duplicates() (in module slideflow.Dataset) checkpoint_to_tf_model() (in module slideflow.io.tensorflow) choice_input() (in module slideflow.util) CLAMModelConfig (class in slideflow.clam) class_interpolate() (StyleGAN2Interpolator method) clear_filters() (in module slideflow.Dataset) clear_insets() (in module slideflow.Heatmap) clear_message() (Studio method) clear_model_results() (Studio method) clear_overlay() (Studio method) clear_result() (Studio method) clear_status_message() (Studio method) clip() (in module slideflow.Dataset) close() (Studio method) close_model() (Studio method) close_slide() (Studio method) cluster() (in module slideflow.SlideMap) collapsing_header() (Studio method) collapsing_header2() (Studio method) comparison_plot() (in module slideflow.grad) concat() (in module slideflow.DatasetFeatures) content_width (Sidebar property) convert_dtype() (in module slideflow.io) convert_xml_rois() (in module slideflow.Dataset) create_blank_annotations() (in module slideflow.Project) create_hp_sweep() (in module slideflow.Project) create_project() (in module slideflow) create_triangles() (in module slideflow.util) crop() (in module slideflow.gan.utils) D Dataset (class in slideflow) dataset() (in module slideflow.Project) DatasetBuilder (class in slideflow.simclr) DatasetFeatures (class in slideflow) decode_image() (in module slideflow.io.tensorflow) decrease_tile_zoom() (Studio method) default() (ValidJSONEncoder method) defer_rendering() (Studio method) delong_roc_test() (in module slideflow.biscuit.delong) delong_roc_variance() (in module slideflow.biscuit.delong) detect() (in module slideflow.biscuit.threshold) detect_tfrecord_format() (in module slideflow.io) df_from_cv() (in module slideflow.biscuit.utils) df_from_pred() (in module slideflow.stats) dim_text() (Studio method) dim_to_mpp() (in module slideflow.WSI) display() (in module slideflow.biscuit.Experiment) download_from_tcga() (in module slideflow.util) draw() (Sidebar method) draw_frame() (Studio method) E EasyDict (class in slideflow.util) eval() (in module slideflow.mil.TrainerConfig) eval_dataset() (in module slideflow.stats) eval_exists() (in module slideflow.biscuit.utils) eval_mil() (in module slideflow.mil) evaluate() (in module slideflow.model.Trainer) (in module slideflow.Project) evaluate_mil() (in module slideflow.Project) Experiment (class in slideflow.biscuit) export_rois() (in module slideflow.WSI) extract_cells() (in module slideflow.Dataset) (in module slideflow.Project) (in module slideflow.WSI) extract_centroids() (in module slideflow.cellseg.Segmentation) extract_tiles() (in module slideflow.Dataset) (in module slideflow.io) (in module slideflow.Project) (in module slideflow.WSI) extract_tiles_from_tfrecords() (in module slideflow.Dataset) F fastDeLong() (in module slideflow.biscuit.delong) FeatureExtractionProgress (class in slideflow.util) Features (class in slideflow.model) filter() (in module slideflow.Dataset) (in module slideflow.SlideMap) find_cv() (in module slideflow.biscuit) (in module slideflow.biscuit.utils) find_cv_early_stop() (in module slideflow.biscuit.utils) find_eval() (in module slideflow.biscuit.utils) find_model() (in module slideflow.biscuit.utils) find_slide() (in module slideflow.Dataset) find_tfrecord() (in module slideflow.Dataset) fit() (in module slideflow.norm.StainNormalizer) flatten() (in module slideflow.model.tensorflow) from_cv() (in module slideflow.biscuit.threshold) from_df() (in module slideflow.DatasetFeatures) from_model() (in module slideflow.model.Features) full_button() (Sidebar method) full_button2() (Sidebar method) full_width (Sidebar property) G gan_generate() (in module slideflow.Project) gan_train() (in module slideflow.Project) Gaussian (class in slideflow.slide.qc) generate() (in module slideflow.Heatmap) (StyleGAN2Interpolator method) generate_attention_heatmaps() (in module slideflow.mil) generate_crossfolds() (in module slideflow.io.preservedsite) generate_end() (StyleGAN2Interpolator method) generate_feature_bags() (in module slideflow.Dataset) (in module slideflow.Project) generate_features() (in module slideflow.Project) generate_grid() (in module slideflow.Mosaic) generate_heatmaps() (in module slideflow.Project) generate_mil_features() (in module slideflow.mil) generate_mosaic() (in module slideflow.Project) generate_mosaic_from_annotations() (in module slideflow.Project) generate_np_end() (StyleGAN2Interpolator method) generate_np_from_embedding() (StyleGAN2Interpolator method) generate_np_start() (StyleGAN2Interpolator method) generate_start() (StyleGAN2Interpolator method) generate_tf_end() (StyleGAN2Interpolator method) generate_tf_from_embedding() (StyleGAN2Interpolator method) generate_tf_start() (StyleGAN2Interpolator method) generate_tfrecord_heatmap() (in module slideflow.Project) get_args() (in module slideflow.simclr) get_bags() (in module slideflow.Dataset) get_centroid_index() (in module slideflow.stats) get_default_widgets() (Studio static method) get_ensemble_model_config() (in module slideflow.util) get_eval_results() (in module slideflow.biscuit.utils) get_extension() (Studio method) get_fit() (in module slideflow.norm.StainNormalizer) get_gan_config() (in module slideflow.util) get_locations_from_tfrecord() (in module slideflow.io) get_metrics() (in module slideflow.mil.TrainerConfig) get_mil_tile_predictions() (in module slideflow.mil) get_model_config() (in module slideflow.util) get_model_normalizer() (in module slideflow.util) get_model_results() (in module slideflow.biscuit) (in module slideflow.biscuit.utils) get_normalizer() (in module slideflow.ModelParams) get_preprocess_fn() (in module slideflow.util) get_relative_tfrecord_paths() (in module slideflow.util) get_renderables() (FeatureExtractionProgress method) (TileExtractionProgress method) get_renderer() (Studio method) get_slide_paths() (in module slideflow.util) get_slides_from_model_manifest() (in module slideflow.util) get_tfrecord_by_index() (in module slideflow.io) get_tfrecord_by_location() (in module slideflow.io) get_tfrecord_length() (in module slideflow.io) get_tfrecord_locations() (in module slideflow.Dataset) get_tfrecord_parser() (in module slideflow.io) (in module slideflow.io.tensorflow) get_tile_dataframe() (in module slideflow.Dataset) (in module slideflow.WSI) get_tile_mask() (in module slideflow.WSI) get_valid_model_dir() (in module slideflow.util) get_widget() (Studio method) getLoggingLevel() (in module slideflow) (in module slideflow.util) global_path() (in module slideflow.util) gradcam() (SaliencyMap method) grayscale() (in module slideflow.grad) group_reduce() (in module slideflow.stats) guided_integrated_gradients() (SaliencyMap method) H harmonize_labels() (in module slideflow.Dataset) has_live_viewer() (Studio method) has_rois() (in module slideflow.WSI) has_uq() (Studio method) header() (Studio method) header_with_buttons() (Studio method) Heatmap (class in slideflow) highlighted() (Studio method) I ImgBatchSpeedColumn (class in slideflow.util) increase_tile_zoom() (Studio method) IndexedInterleaver (class in slideflow.io.torch) infer_stride() (in module slideflow.util) inferno() (in module slideflow.grad) inspect_batch() (in module slideflow.mil.MILModelConfig) (in module slideflow.mil.TrainerConfig) integrated_gradients() (SaliencyMap method) interleave() (in module slideflow.io.tensorflow) InterleaveIterator (class in slideflow.io.torch) interpolate_and_predict() (StyleGAN2Interpolator method) is_classification() (in module slideflow.mil.MILModelConfig) (in module slideflow.mil.TrainerConfig) is_float() (in module slideflow.Dataset) is_model() (in module slideflow.util) is_mouse_down() (Studio method) is_mouse_released() (Studio method) is_project() (in module slideflow.util) is_simclr_model_path() (in module slideflow.util) is_slide() (in module slideflow.util) is_tensorflow_model() (in module slideflow.model) is_tensorflow_model_path() (in module slideflow.util) is_tensorflow_tensor() (in module slideflow.model) is_tile_size_compatible() (in module slideflow.util) is_torch_model() (in module slideflow.model) is_torch_model_path() (in module slideflow.util) is_torch_tensor() (in module slideflow.model) is_uq_model() (in module slideflow.util) isnumeric() (in module slideflow.util) J join_tfrecord() (in module slideflow.io.tensorflow) jpeg_to_jpeg() (in module slideflow.norm.StainNormalizer) jpeg_to_rgb() (in module slideflow.norm.StainNormalizer) json_dump() (in module slideflow.mil.TrainerConfig) K kfold_split() (in module slideflow.Dataset) L label() (in module slideflow.SlideMap) label_by_preds() (in module slideflow.SlideMap) label_by_slide() (in module slideflow.SlideMap) label_by_uncertainty() (in module slideflow.SlideMap) LabeledMofNCompleteColumn (class in slideflow.util) labels() (in module slideflow.Dataset) large_image_button() (Sidebar method) lazy_load_pretrained() (in module slideflow.model.torch) linear_interpolate() (StyleGAN2Interpolator method) list_extractors() (in module slideflow.model) Load (class in slideflow.slide.qc) load() (in module slideflow.Heatmap) (in module slideflow.model) (in module slideflow.model.tensorflow) (in module slideflow.model.torch) (in module slideflow.model.Trainer) (in module slideflow.simclr) (in module slideflow.SlideMap) load_annotations() (in module slideflow.Dataset) load_cache() (in module slideflow.DatasetFeatures) load_coordinates() (in module slideflow.SlideMap) load_csv_roi() (in module slideflow.WSI) load_heatmap() (Studio method) load_indices() (in module slideflow.Dataset) load_json() (in module slideflow.util) load_json_roi() (in module slideflow.WSI) load_model() (Studio method) load_model_args() (in module slideflow.simclr) load_npz() (in module slideflow.Heatmap) load_predictions() (in module slideflow.util) load_project() (in module slideflow) (Studio method) load_roi_array() (in module slideflow.WSI) load_slide() (Studio method) load_umap() (in module slideflow.SlideMap) location_heatmap() (in module slideflow.util) log_manifest() (in module slideflow.model.tensorflow) (in module slideflow.model.torch) (in module slideflow.util) M make_dir() (in module slideflow.util) manifest() (in module slideflow.Dataset) manifest_histogram() (in module slideflow.Dataset) map_activations() (in module slideflow.DatasetFeatures) map_predictions() (in module slideflow.DatasetFeatures) map_values_to_slide_grid() (in module slideflow.util) mask_to_image() (in module slideflow.cellseg.Segmentation) md5() (in module slideflow.util) merge() (in module slideflow.DatasetFeatures) metrics_from_dataset() (in module slideflow.stats) mil_config() (in module slideflow.mil) MILModelConfig (class in slideflow.mil) model (Studio property) model_exists() (in module slideflow.biscuit.utils) model_type() (in module slideflow.ModelParams) ModelParams (class in slideflow) module slideflow.gan slideflow.gan.utils slideflow.grad slideflow.io.tensorflow slideflow.io.torch slideflow.studio slideflow.util Mosaic (class in slideflow) mouse_input_is_suspended() (Studio method) mouse_is_over_viewer (Studio property) mpp_to_dim() (in module slideflow.WSI) multi_image_example() (in module slideflow.io.tensorflow) multi_plot() (in module slideflow.grad) multi_warn() (in module slideflow.util) MultiprocessProgress (class in slideflow.util) MultiprocessProgressTracker (class in slideflow.util) N name_columns() (in module slideflow.stats) nature2022() (in module slideflow.biscuit.hp) neighbors() (in module slideflow.SlideMap) noise_tensor() (in module slideflow.gan.utils) O offset_x (Studio property) offset_x_pixels (Studio property) offset_y (Studio property) offset_y_pixels (Studio property) oranges() (in module slideflow.grad) Otsu (class in slideflow.slide.qc) outline_to_image() (in module slideflow.cellseg.Segmentation) overlay() (in module slideflow.grad) P P (Studio property) 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() (in module slideflow.Dataset) plot() (in module slideflow.Heatmap) (in module slideflow.Mosaic) (in module slideflow.SlideMap) plot_3d() (in module slideflow.SlideMap) plot_comparison() (StyleGAN2Interpolator method) plot_thumbnail() (in module slideflow.Heatmap) plot_uncertainty() (in module slideflow.biscuit.threshold) (in module slideflow.Heatmap) plot_uq_calibration() (in module slideflow.biscuit.Experiment) plot_with_logit_cmap() (in module slideflow.Heatmap) png_to_png() (in module slideflow.norm.StainNormalizer) png_to_rgb() (in module slideflow.norm.StainNormalizer) points_at_grid_index() (in module slideflow.Mosaic) predict() (in module slideflow.mil.MILModelConfig) (in module slideflow.mil.TrainerConfig) (in module slideflow.model.Trainer) (in module slideflow.Project) (in module slideflow.slide) (in module slideflow.WSI) predict_dataset() (in module slideflow.stats) predict_ensemble() (in module slideflow.Project) predict_from_bags() (in module slideflow.mil) predict_from_multimodal_bags() (in module slideflow.mil) predict_mil() (in module slideflow.mil) predict_multimodal_mil() (in module slideflow.mil) predict_slide() (in module slideflow.mil) predict_wsi() (in module slideflow.Project) prediction_metrics() (in module slideflow.biscuit.utils) prepare_training() (in module slideflow.mil.TrainerConfig) preprocess_uint8() (in module slideflow.io.tensorflow) preview() (in module slideflow.WSI) print_error() (Studio method) print_tfrecord() (in module slideflow.io.tensorflow) process_group_predictions() (in module slideflow.biscuit.threshold) process_image() (in module slideflow.io.tensorflow) process_rois() (in module slideflow.WSI) process_tile_predictions() (in module slideflow.biscuit.threshold) Project (class in slideflow) Q qc() (in module slideflow.WSI) R read_and_return_record() (in module slideflow.io) (in module slideflow.io.tensorflow) read_annotations() (in module slideflow.util) read_group_predictions() (in module slideflow.biscuit.utils) read_hp_sweep() (in module slideflow.model) read_tfrecord_by_location() (in module slideflow.Dataset) rebuild_extractor() (in module slideflow.model) rebuild_index() (in module slideflow.Dataset) RegressionTrainer (class in slideflow.model) relative_path() (in module slideflow.util) reload_model() (Studio method) reload_viewer() (Studio method) reload_wsi() (Studio method) remove_filter() (in module slideflow.Dataset) remove_from_render_pipeline() (Studio method) remove_qc() (in module slideflow.WSI) remove_roi() (in module slideflow.WSI) remove_slide() (in module slideflow.DatasetFeatures) remove_widget() (Sidebar method) (Studio method) render() (ImgBatchSpeedColumn method) (LabeledMofNCompleteColumn method) (TileExtractionSpeedColumn method) reset_background() (Studio method) reset_tile_zoom() (Studio method) resize_tfrecords() (in module slideflow.Dataset) results() (in module slideflow.biscuit.Experiment) resume_keyboard_input() (Studio method) resume_mouse_input_handling() (Studio method) rgb_to_rgb() (in module slideflow.norm.StainNormalizer) rois() (in module slideflow.Dataset) run_metrics() (in module slideflow.mil.MILModelConfig) (in module slideflow.mil.TrainerConfig) run_simclr() (in module slideflow.simclr) S saliency_map_comparison() (in module slideflow.grad) SaliencyMap (class in slideflow.grad) Save (class in slideflow.slide.qc) save() (in module slideflow.cellseg.Segmentation) (in module slideflow.Heatmap) (in module slideflow.Mosaic) (in module slideflow.Project) (in module slideflow.SlideMap) save_3d() (in module slideflow.SlideMap) save_cache() (in module slideflow.DatasetFeatures) save_coordinates() (in module slideflow.SlideMap) save_encoder() (in module slideflow.SlideMap) save_example_tiles() (in module slideflow.DatasetFeatures) save_npz() (in module slideflow.Heatmap) save_plot() (in module slideflow.SlideMap) save_report() (in module slideflow.Mosaic) save_umap() (in module slideflow.SlideMap) seed_search() (StyleGAN2Interpolator method) segment_slide() (in module slideflow.cellseg) Segmentation (class in slideflow.cellseg) serialized_record() (in module slideflow.io) (in module slideflow.io.tensorflow) set_classifier() (StyleGAN2Interpolator method) set_fit() (in module slideflow.norm.StainNormalizer) set_grid_overlay() (Studio method) set_ignore_sigint() (in module slideflow.util) set_message() (Studio method) set_overlay() (Studio method) set_prediction_message() (Studio method) set_status_message() (Studio method) set_viewer() (Studio method) setLoggingLevel() (in module slideflow) (in module slideflow.util) show_alignment() (in module slideflow.WSI) show_overlay (Studio property) shuffle_tfrecord() (in module slideflow.io.tensorflow) shuffle_tfrecords_by_dir() (in module slideflow.io.tensorflow) Sidebar (class in slideflow.studio) SimCLR (class in slideflow.simclr) SimCLR_Args (class in slideflow.simclr) slide_manifest() (in module slideflow.Dataset) slide_paths() (in module slideflow.Dataset) slideflow.gan module slideflow.gan.utils module slideflow.grad module slideflow.io.tensorflow module slideflow.io.torch module slideflow.studio module slideflow.util module SlideMap (class in slideflow) slides() (in module slideflow.Dataset) smac_search() (in module slideflow.Project) small_button() (Sidebar method) softmax_mean() (in module slideflow.DatasetFeatures) softmax_percent() (in module slideflow.DatasetFeatures) softmax_predict() (in module slideflow.DatasetFeatures) split() (in module slideflow.Dataset) split_list() (in module slideflow.util) split_tfrecord() (in module slideflow.io.tensorflow) split_tfrecords_by_roi() (in module slideflow.Dataset) square_thumb() (in module slideflow.WSI) StainNormalizer (class in slideflow.norm) stats() (in module slideflow.DatasetFeatures) StridedDL (class in slideflow.slide.qc) Studio (class in slideflow.studio) StyleGAN2Interpolator (class in slideflow.gan) summary() (in module slideflow.Dataset) SurvivalTrainer (class in slideflow.model) suspend_keyboard_input() (Studio method) suspend_mouse_input_handling() (Studio method) T tensorflow() (in module slideflow.Dataset) (in module slideflow.WSI) tf_to_rgb() (in module slideflow.norm.StainNormalizer) tf_to_tf() (in module slideflow.norm.StainNormalizer) tfrecord_example() (in module slideflow.io.tensorflow) tfrecord_has_locations() (in module slideflow.io) tfrecord_heatmap() (in module slideflow.Dataset) (in module slideflow.util) tfrecord_report() (in module slideflow.Dataset) tfrecords() (in module slideflow.Dataset) tfrecords_by_subfolder() (in module slideflow.Dataset) tfrecords_folders() (in module slideflow.Dataset) tfrecords_from_tiles() (in module slideflow.Dataset) tfrecords_have_locations() (in module slideflow.Dataset) theme (Sidebar property) thresholds_from_nested_cv() (in module slideflow.biscuit.Experiment) thumb() (in module slideflow.WSI) thumbnails() (in module slideflow.Dataset) tile_preview_enabled (Studio property) tile_size_label() (in module slideflow.util) TileExtractionProgress (class in slideflow.util) TileExtractionSpeedColumn (class in slideflow.util) to_csv() (in module slideflow.DatasetFeatures) to_df() (in module slideflow.DatasetFeatures) to_dict() (in module slideflow.mil.MILModelConfig) (in module slideflow.mil.TrainerConfig) (in module slideflow.ModelParams) to_onehot() (in module slideflow.util) to_torch() (in module slideflow.DatasetFeatures) torch() (in module slideflow.Dataset) (in module slideflow.WSI) torch_to_torch() (in module slideflow.norm.StainNormalizer) train() (in module slideflow.biscuit.Experiment) (in module slideflow.mil.TrainerConfig) (in module slideflow.model.Trainer) (in module slideflow.Project) train_ensemble() (in module slideflow.Project) train_mil() (in module slideflow.mil) (in module slideflow.Project) train_nested_cv() (in module slideflow.biscuit.Experiment) train_simclr() (in module slideflow.Project) Trainer (class in slideflow.model) TrainerConfig (class in slideflow.mil) transform() (in module slideflow.norm.StainNormalizer) transform_tfrecord() (in module slideflow.io.tensorflow) transform_tfrecords() (in module slideflow.Dataset) truncate_colormap() (in module slideflow.biscuit.utils) U umap_transform() (in module slideflow.SlideMap) unclip() (in module slideflow.Dataset) unwrap() (in module slideflow.model.tensorflow) update_annotations_with_slidenames() (in module slideflow.Dataset) update_manifest() (in module slideflow.Dataset) update_manifest_at_dir() (in module slideflow.io) update_results_log() (in module slideflow.util) V validate() (in module slideflow.ModelParams) ValidJSONEncoder (class in slideflow.util) vanilla() (SaliencyMap method) verify_alignment() (in module slideflow.WSI) verify_annotations_slides() (in module slideflow.Dataset) verify_img_format() (in module slideflow.Dataset) verify_slide_names() (in module slideflow.Dataset) view() (in module slideflow.Heatmap) (in module slideflow.Mosaic) (in module slideflow.WSI) W write_json() (in module slideflow.util) write_tfrecords_merge() (in module slideflow.io) write_tfrecords_multi() (in module slideflow.io) write_tfrecords_single() (in module slideflow.io) WSI (class in slideflow.slide) X xrai() (SaliencyMap method) xrai_fast() (SaliencyMap method) Y yes_no_input() (in module slideflow.util) Z z() (StyleGAN2Interpolator method)