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) (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) blur_integrated_gradients() (SaliencyMap method) box_plots() (in module slideflow.DatasetFeatures) build_fastai_learner() (in module slideflow.mil) build_feature_extractor() (in module slideflow.model) build_generator() (in module slideflow.WSI) build_index() (in module slideflow.Dataset) build_mosaic() (in module slideflow.SlideMap) build_trainer() (in module slideflow.model) 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) 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) 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) CPHTrainer (class in slideflow.model) create_blank_annotations() (in module slideflow.Project) create_hp_sweep() (in module slideflow.Project) create_project() (in module slideflow) 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) 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_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_clam() (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) 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_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_crossfolds() (in module slideflow.io.preservedsite) generate_end() (StyleGAN2Interpolator method) generate_feature_bags() (in module slideflow.Project) generate_features() (in module slideflow.Project) generate_grid() (in module slideflow.Mosaic) generate_heatmaps() (in module slideflow.Project) 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_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_fit() (in module slideflow.norm.StainNormalizer) get_gan_config() (in module slideflow.util) get_locations_from_tfrecord() (in module slideflow.io) 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() (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) inferno() (in module slideflow.grad) integrated_gradients() (SaliencyMap method) interleave() (in module slideflow.io.tensorflow) InterleaveIterator (class in slideflow.io.torch) interpolate_and_predict() (StyleGAN2Interpolator method) is_float() (in module slideflow.Dataset) is_model() (in module slideflow.util) 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_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.TrainerConfigCLAM) (in module slideflow.mil.TrainerConfigFastAI) 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) labels() (in module slideflow.Dataset) large_image_button() (Sidebar method) lazy_load_pretrained() (in module slideflow.model.torch) linear_interpolate() (StyleGAN2Interpolator method) LinearTrainer (class in slideflow.model) 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) model (Studio property) model_exists() (in module slideflow.biscuit.utils) model_type() (in module slideflow.ModelParams) ModelConfigCLAM (class in slideflow.mil) ModelConfigFastAI (class in slideflow.mil) 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) 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) 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.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_slide() (in module slideflow.mil) predict_wsi() (in module slideflow.Project) prediction_metrics() (in module slideflow.biscuit.utils) 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) pt_files() (in module slideflow.Dataset) 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) relative_path() (in module slideflow.util) reload_model() (Studio method) reload_viewer() (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) (TileExtractionSpeedColumn method) reset_background() (Studio method) reset_tile_zoom() (Studio method) resize_tfrecords() (in module slideflow.Dataset) results() (in module slideflow.biscuit.Experiment) rgb_to_rgb() (in module slideflow.norm.StainNormalizer) rois() (in module slideflow.Dataset) 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_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) 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) 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.TrainerConfigCLAM) (in module slideflow.mil.TrainerConfigFastAI) (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.model.Trainer) (in module slideflow.Project) train_clam() (in module slideflow.mil) (in module slideflow.Project) train_ensemble() (in module slideflow.Project) train_fastai() (in module slideflow.mil) 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) TrainerConfigCLAM (class in slideflow.mil) TrainerConfigFastAI (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) 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)