Index

_

__call__() (in module model.Features)

__init__() (histox.io.torch.IndexedInterleaver method) (histox.io.torch.InterleaveIterator method)

A

about() (in module histox) (in module histox.util) activations() (in module SlideMap) activations_by_category() (in module DatasetFeatures) add_inset() (in module Heatmap) add_source() (in module Project) add_to_render_pipeline() (histox.studio.Studio method) add_widgets() (histox.studio.Sidebar method) (histox.studio.Studio method) align_tiles_to() (in module WSI) align_to() (in module WSI) all() (histox.grad.SaliencyMap method) apply() (in module biscuit.threshold)

apply_qc_mask() (in module WSI) apply_rois() (in module cellseg.Segmentation) apply_segmentation() (in module WSI) area() (in module WSI) ask_load_heatmap() (histox.studio.Studio method) ask_load_model() (histox.studio.Studio method) ask_load_project() (histox.studio.Studio method) ask_load_slide() (histox.studio.Studio method) ask_zoom_to_mpp() (histox.studio.Studio method) associate_slide_names() (in module Project) auc() (in module biscuit.utils) auc_and_threshold() (in module biscuit.utils) augment() (in module norm.StainNormalizer) autoload() (histox.studio.Studio method)

B

balance() (in module Dataset) batch() (in module histox.util) batch_generator() (in module histox.util) batched_predict() (in module mil.MILModelConfig) (in module mil.TrainerConfig) bin_values_to_slide_grid() (in module histox.util) blur_integrated_gradients() (histox.grad.SaliencyMap method) box_plots() (in module DatasetFeatures) build_fastai_learner() (in module histox.mil) build_feature_extractor() (in module histox) (in module histox.model)

build_generator() (in module WSI) build_index() (in module Dataset) build_model() (in module mil.MILModelConfig) (in module mil.TrainerConfig) build_mosaic() (in module SlideMap) build_multimodal_learner() (in module histox.mil) build_parser() (histox.io.torch.IndexedInterleaver method) build_train_dataloader() (in module mil.TrainerConfig) build_trainer() (in module histox.model) build_val_dataloader() (in module mil.TrainerConfig)

C

calculate_centroid() (in module histox.stats) calculate_centroids() (in module cellseg.Segmentation) calculate_outlines() (in module cellseg.Segmentation) cell_segmentation() (in module Dataset) (in module Project) center_next_window() (histox.studio.Studio method) centroid_to_image() (in module cellseg.Segmentation) centroids() (in module cellseg.Segmentation) check_duplicates() (in module Dataset) checkpoint_to_tf_model() (in module histox.io.tensorflow) choice_input() (in module histox.util) CLAMModelConfig (in module clam) class_interpolate() (histox.gan.StyleGAN2Interpolator method) clear_filters() (in module Dataset) clear_insets() (in module Heatmap) clear_message() (histox.studio.Studio method) clear_model_results() (histox.studio.Studio method) clear_overlay() (histox.studio.Studio method)

clear_result() (histox.studio.Studio method) clear_status_message() (histox.studio.Studio method) clip() (in module Dataset) close() (histox.studio.Studio method) close_model() (histox.studio.Studio method) close_slide() (histox.studio.Studio method) cluster() (in module SlideMap) collapsing_header() (histox.studio.Studio method) collapsing_header2() (histox.studio.Studio method) comparison_plot() (in module histox.grad) concat() (in module DatasetFeatures) content_width (histox.studio.Sidebar property) convert_dtype() (in module histox.io) convert_xml_rois() (in module Dataset) create_blank_annotations() (in module Project) create_hp_sweep() (in module Project) create_project() (in module histox) create_triangles() (in module histox.util) crop() (in module histox.gan.utils)

D

Dataset (class in histox) dataset() (in module Project) DatasetBuilder (in module simclr) DatasetFeatures (class in histox) decode_image() (in module histox.io.tensorflow) decrease_tile_zoom() (histox.studio.Studio method) default() (histox.util.ValidJSONEncoder method) defer_rendering() (histox.studio.Studio method) delong_roc_test() (in module biscuit.delong) delong_roc_variance() (in module biscuit.delong)

detect() (in module biscuit.threshold) detect_tfrecord_format() (in module histox.io) df_from_cv() (in module biscuit.utils) df_from_pred() (in module histox.stats) dim_text() (histox.studio.Studio method) dim_to_mpp() (in module WSI) display() (in module biscuit.Experiment) download_from_tcga() (in module histox.util) draw() (histox.studio.Sidebar method) draw_frame() (histox.studio.Studio method)

E

EasyDict (class in histox.util) eval() (in module mil.TrainerConfig) eval_dataset() (in module histox.stats) eval_exists() (in module biscuit.utils) eval_mil() (in module histox.mil) evaluate() (in module model.Trainer) (in module Project) evaluate_mil() (in module Project) Experiment (in module histox.biscuit)

export_rois() (in module WSI) extract_cells() (in module Dataset) (in module Project) (in module WSI) extract_centroids() (in module cellseg.Segmentation) extract_tiles() (in module Dataset) (in module histox.io) (in module Project) (in module WSI) extract_tiles_from_tfrecords() (in module Dataset)

F

fastDeLong() (in module biscuit.delong) FeatureExtractionProgress (class in histox.util) Features (class in histox.model) filter() (in module Dataset) (in module SlideMap) find_cv() (in module biscuit.utils) (in module histox.biscuit) find_cv_early_stop() (in module biscuit.utils) find_eval() (in module biscuit.utils) find_model() (in module biscuit.utils)

find_slide() (in module Dataset) find_tfrecord() (in module Dataset) fit() (in module norm.StainNormalizer) flatten() (in module model.tensorflow) from_cv() (in module biscuit.threshold) from_df() (in module DatasetFeatures) from_model() (in module model.Features) full_button() (histox.studio.Sidebar method) full_button2() (histox.studio.Sidebar method) full_width (histox.studio.Sidebar property)

G

gan_generate() (in module Project) gan_train() (in module Project) Gaussian (class in histox.slide.qc) generate() (histox.gan.StyleGAN2Interpolator method) (in module Heatmap) generate_attention_heatmaps() (in module histox.mil) generate_crossfolds() (in module io.preservedsite) generate_end() (histox.gan.StyleGAN2Interpolator method) generate_feature_bags() (in module Dataset) (in module Project) generate_features() (in module Project) generate_grid() (in module Mosaic) generate_heatmaps() (in module Project) generate_mil_features() (in module histox.mil) generate_mosaic() (in module Project) generate_mosaic_from_annotations() (in module Project) generate_np_end() (histox.gan.StyleGAN2Interpolator method) generate_np_from_embedding() (histox.gan.StyleGAN2Interpolator method) generate_np_start() (histox.gan.StyleGAN2Interpolator method) generate_start() (histox.gan.StyleGAN2Interpolator method) generate_tf_end() (histox.gan.StyleGAN2Interpolator method) generate_tf_from_embedding() (histox.gan.StyleGAN2Interpolator method) generate_tf_start() (histox.gan.StyleGAN2Interpolator method) generate_tfrecord_heatmap() (in module Project) get_args() (in module simclr) get_bags() (in module Dataset) get_centroid_index() (in module histox.stats) get_default_widgets() (histox.studio.Studio static method) get_ensemble_model_config() (in module histox.util) get_eval_results() (in module biscuit.utils) get_extension() (histox.studio.Studio method) get_fit() (in module norm.StainNormalizer) get_gan_config() (in module histox.util)

get_locations_from_tfrecord() (in module histox.io) get_metrics() (in module mil.TrainerConfig) get_mil_tile_predictions() (in module histox.mil) get_model_config() (in module histox.util) get_model_normalizer() (in module histox.util) get_model_results() (in module biscuit.utils) (in module histox.biscuit) get_normalizer() (in module ModelParams) get_preprocess_fn() (in module histox.util) get_relative_tfrecord_paths() (in module histox.util) get_renderables() (histox.util.FeatureExtractionProgress method) (histox.util.TileExtractionProgress method) get_renderer() (histox.studio.Studio method) get_slide_paths() (in module histox.util) get_slides_from_model_manifest() (in module histox.util) get_tfrecord_by_index() (in module histox.io) get_tfrecord_by_location() (in module histox.io) get_tfrecord_length() (in module histox.io) get_tfrecord_locations() (in module Dataset) get_tfrecord_parser() (in module histox.io) (in module histox.io.tensorflow) get_tile_dataframe() (in module Dataset) (in module WSI) get_tile_mask() (in module WSI) get_valid_model_dir() (in module histox.util) get_widget() (histox.studio.Studio method) getLoggingLevel() (in module histox) (in module histox.util) global_path() (in module histox.util) gradcam() (histox.grad.SaliencyMap method) grayscale() (in module histox.grad) group_reduce() (in module histox.stats) guided_integrated_gradients() (histox.grad.SaliencyMap method)

H

harmonize_labels() (in module Dataset) has_live_viewer() (histox.studio.Studio method) has_rois() (in module WSI) has_uq() (histox.studio.Studio method) header() (histox.studio.Studio method) header_with_buttons() (histox.studio.Studio method) Heatmap (class in histox) highlighted() (histox.studio.Studio method) histox.gan module histox.gan.utils module

histox.grad module histox.io.tensorflow module histox.io.torch module histox.studio module histox.util module

I

ImgBatchSpeedColumn (class in histox.util) increase_tile_zoom() (histox.studio.Studio method) IndexedInterleaver (class in histox.io.torch) infer_stride() (in module histox.util) inferno() (in module histox.grad) inspect_batch() (in module mil.MILModelConfig) (in module mil.TrainerConfig) integrated_gradients() (histox.grad.SaliencyMap method) interleave() (in module histox.io.tensorflow) InterleaveIterator (class in histox.io.torch) interpolate_and_predict() (histox.gan.StyleGAN2Interpolator method) is_classification() (in module mil.MILModelConfig) (in module mil.TrainerConfig) is_float() (in module Dataset)

is_model() (in module histox.util) is_mouse_down() (histox.studio.Studio method) is_mouse_released() (histox.studio.Studio method) is_project() (in module histox.util) is_simclr_model_path() (in module histox.util) is_slide() (in module histox.util) is_tensorflow_model() (in module histox.model) is_tensorflow_model_path() (in module histox.util) is_tensorflow_tensor() (in module histox.model) is_tile_size_compatible() (in module histox.util) is_torch_model() (in module histox.model) is_torch_model_path() (in module histox.util) is_torch_tensor() (in module histox.model) is_uq_model() (in module histox.util) isnumeric() (in module histox.util)

J

join_tfrecord() (in module histox.io.tensorflow) jpeg_to_jpeg() (in module norm.StainNormalizer)

jpeg_to_rgb() (in module norm.StainNormalizer) json_dump() (in module mil.TrainerConfig)

K

kfold_split() (in module Dataset)

L

label() (in module SlideMap) label_by_preds() (in module SlideMap) label_by_slide() (in module SlideMap) label_by_uncertainty() (in module SlideMap) LabeledMofNCompleteColumn (class in histox.util) labels() (in module Dataset) large_image_button() (histox.studio.Sidebar method) lazy_load_pretrained() (in module model.torch) linear_interpolate() (histox.gan.StyleGAN2Interpolator method) list_extractors() (in module histox.model) Load (class in histox.slide.qc) load() (in module Heatmap) (in module histox.model) (in module model.tensorflow) (in module model.torch) (in module model.Trainer) (in module simclr) (in module SlideMap) load_annotations() (in module Dataset)

load_cache() (in module DatasetFeatures) load_coordinates() (in module SlideMap) load_csv_roi() (in module WSI) load_heatmap() (histox.studio.Studio method) load_indices() (in module Dataset) load_json() (in module histox.util) load_json_roi() (in module WSI) load_model() (histox.studio.Studio method) load_model_args() (in module simclr) load_npz() (in module Heatmap) load_predictions() (in module histox.util) load_project() (histox.studio.Studio method) (in module histox) load_roi_array() (in module WSI) load_slide() (histox.studio.Studio method) load_umap() (in module SlideMap) location_heatmap() (in module histox.util) log_manifest() (in module histox.util) (in module model.tensorflow) (in module model.torch)

M

make_dir() (in module histox.util) manifest() (in module Dataset) manifest_histogram() (in module Dataset) map_activations() (in module DatasetFeatures) map_predictions() (in module DatasetFeatures) map_values_to_slide_grid() (in module histox.util) mask_to_image() (in module cellseg.Segmentation) md5() (in module histox.util) merge() (in module DatasetFeatures) metrics_from_dataset() (in module histox.stats) mil_config() (in module histox.mil) MILModelConfig (class in histox.mil) model (histox.studio.Studio property) model_exists() (in module biscuit.utils) model_type() (in module ModelParams) ModelParams (class in histox)

module histox.gan histox.gan.utils histox.grad histox.io.tensorflow histox.io.torch histox.studio histox.util Mosaic (class in histox) mouse_input_is_suspended() (histox.studio.Studio method) mouse_is_over_viewer (histox.studio.Studio property) mpp_to_dim() (in module WSI) multi_image_example() (in module histox.io.tensorflow) multi_plot() (in module histox.grad) multi_warn() (in module histox.util) MultiprocessProgress (class in histox.util) MultiprocessProgressTracker (class in histox.util)

N

name_columns() (in module histox.stats) nature2022() (in module biscuit.hp)

neighbors() (in module SlideMap) noise_tensor() (in module histox.gan.utils)

O

offset_x (histox.studio.Studio property) offset_x_pixels (histox.studio.Studio property) offset_y (histox.studio.Studio property) offset_y_pixels (histox.studio.Studio property)

oranges() (in module histox.grad) Otsu (class in histox.slide.qc) outline_to_image() (in module cellseg.Segmentation) overlay() (in module histox.grad)

P

P (histox.studio.Studio property) parser_from_labels() (in module histox.io.tensorflow) path_input() (in module histox.util) path_to_ext() (in module histox.util) path_to_name() (in module histox.util) patients() (in module Dataset) plot() (in module Heatmap) (in module Mosaic) (in module SlideMap) plot_3d() (in module SlideMap) plot_comparison() (histox.gan.StyleGAN2Interpolator method) plot_thumbnail() (in module Heatmap) plot_uncertainty() (in module biscuit.threshold) (in module Heatmap) plot_uq_calibration() (in module biscuit.Experiment) plot_with_logit_cmap() (in module Heatmap) png_to_png() (in module norm.StainNormalizer) png_to_rgb() (in module norm.StainNormalizer) points_at_grid_index() (in module Mosaic) predict() (in module mil.MILModelConfig) (in module mil.TrainerConfig) (in module model.Trainer) (in module Project) (in module slide) (in module WSI)

predict_dataset() (in module histox.stats) predict_ensemble() (in module Project) predict_from_bags() (in module histox.mil) predict_from_multimodal_bags() (in module histox.mil) predict_mil() (in module histox.mil) predict_multimodal_mil() (in module histox.mil) predict_slide() (in module histox.mil) predict_wsi() (in module Project) prediction_metrics() (in module biscuit.utils) prepare_training() (in module mil.TrainerConfig) preprocess_uint8() (in module histox.io.tensorflow) preview() (in module WSI) print_error() (histox.studio.Studio method) print_tfrecord() (in module histox.io.tensorflow) process_group_predictions() (in module biscuit.threshold) process_image() (in module histox.io.tensorflow) process_rois() (in module WSI) process_tile_predictions() (in module biscuit.threshold) Project (class in histox)

Q

qc() (in module WSI)

R

read_and_return_record() (in module histox.io) (in module histox.io.tensorflow) read_annotations() (in module histox.util) read_group_predictions() (in module biscuit.utils) read_hp_sweep() (in module histox.model) read_tfrecord_by_location() (in module Dataset) rebuild_extractor() (in module histox.model) rebuild_index() (in module Dataset) RegressionTrainer (class in histox.model) relative_path() (in module histox.util) reload_model() (histox.studio.Studio method) reload_viewer() (histox.studio.Studio method) reload_wsi() (histox.studio.Studio method) remove_filter() (in module Dataset) remove_from_render_pipeline() (histox.studio.Studio method) remove_qc() (in module WSI) remove_roi() (in module WSI)

remove_slide() (in module DatasetFeatures) remove_widget() (histox.studio.Sidebar method) (histox.studio.Studio method) render() (histox.util.ImgBatchSpeedColumn method) (histox.util.LabeledMofNCompleteColumn method) (histox.util.TileExtractionSpeedColumn method) reset_background() (histox.studio.Studio method) reset_tile_zoom() (histox.studio.Studio method) resize_tfrecords() (in module Dataset) results() (in module biscuit.Experiment) resume_keyboard_input() (histox.studio.Studio method) resume_mouse_input_handling() (histox.studio.Studio method) rgb_to_rgb() (in module norm.StainNormalizer) rois() (in module Dataset) run_metrics() (in module mil.MILModelConfig) (in module mil.TrainerConfig) run_simclr() (in module simclr)

S

saliency_map_comparison() (in module histox.grad) SaliencyMap (class in histox.grad) Save (class in histox.slide.qc) save() (in module cellseg.Segmentation) (in module Heatmap) (in module Mosaic) (in module Project) (in module SlideMap) save_3d() (in module SlideMap) save_cache() (in module DatasetFeatures) save_coordinates() (in module SlideMap) save_encoder() (in module SlideMap) save_example_tiles() (in module DatasetFeatures) save_npz() (in module Heatmap) save_plot() (in module SlideMap) save_report() (in module Mosaic) save_umap() (in module SlideMap) seed_search() (histox.gan.StyleGAN2Interpolator method) Segmentation (class in histox.cellseg) serialized_record() (in module histox.io) (in module histox.io.tensorflow) set_classifier() (histox.gan.StyleGAN2Interpolator method) set_fit() (in module norm.StainNormalizer) set_grid_overlay() (histox.studio.Studio method) set_ignore_sigint() (in module histox.util) set_message() (histox.studio.Studio method) set_overlay() (histox.studio.Studio method) set_prediction_message() (histox.studio.Studio method) set_status_message() (histox.studio.Studio method) set_viewer() (histox.studio.Studio method) setLoggingLevel() (in module histox) (in module histox.util)

show_alignment() (in module WSI) show_overlay (histox.studio.Studio property) shuffle_tfrecord() (in module histox.io.tensorflow) shuffle_tfrecords_by_dir() (in module histox.io.tensorflow) Sidebar (class in histox.studio) SimCLR (in module simclr) SimCLR_Args (in module simclr) slide_manifest() (in module Dataset) slide_paths() (in module Dataset) SlideMap (class in histox) slides() (in module Dataset) smac_search() (in module Project) small_button() (histox.studio.Sidebar method) softmax_mean() (in module DatasetFeatures) softmax_percent() (in module DatasetFeatures) softmax_predict() (in module DatasetFeatures) split() (in module Dataset) split_list() (in module histox.util) split_tfrecord() (in module histox.io.tensorflow) split_tfrecords_by_roi() (in module Dataset) square_thumb() (in module WSI) StainNormalizer (class in histox.norm) stats() (in module DatasetFeatures) StridedDL (class in histox.slide.qc) Studio (class in histox.studio) StyleGAN2Interpolator (class in histox.gan) summary() (in module Dataset) SurvivalTrainer (class in histox.model) suspend_keyboard_input() (histox.studio.Studio method) suspend_mouse_input_handling() (histox.studio.Studio method)

T

tensorflow() (in module Dataset) (in module WSI) tf_to_rgb() (in module norm.StainNormalizer) tf_to_tf() (in module norm.StainNormalizer) tfrecord_example() (in module histox.io.tensorflow) tfrecord_has_locations() (in module histox.io) tfrecord_heatmap() (in module Dataset) (in module histox.util) tfrecord_report() (in module Dataset) tfrecords() (in module Dataset) tfrecords_by_subfolder() (in module Dataset) tfrecords_folders() (in module Dataset) tfrecords_from_tiles() (in module Dataset) tfrecords_have_locations() (in module Dataset) theme (histox.studio.Sidebar property) thresholds_from_nested_cv() (in module biscuit.Experiment) thumb() (in module WSI) thumbnails() (in module Dataset) tile_preview_enabled (histox.studio.Studio property) tile_size_label() (in module histox.util) TileExtractionProgress (class in histox.util) TileExtractionSpeedColumn (class in histox.util) to_csv() (in module DatasetFeatures)

to_df() (in module DatasetFeatures) to_dict() (in module mil.MILModelConfig) (in module mil.TrainerConfig) (in module ModelParams) to_onehot() (in module histox.util) to_torch() (in module DatasetFeatures) torch() (in module Dataset) (in module WSI) torch_to_torch() (in module norm.StainNormalizer) train() (in module biscuit.Experiment) (in module mil.TrainerConfig) (in module model.Trainer) (in module Project) train_ensemble() (in module Project) train_mil() (in module histox.mil) (in module Project) train_nested_cv() (in module biscuit.Experiment) train_simclr() (in module Project) Trainer (class in histox.model) TrainerConfig (in module mil) transform() (in module norm.StainNormalizer) transform_tfrecord() (in module histox.io.tensorflow) transform_tfrecords() (in module Dataset) truncate_colormap() (in module biscuit.utils)

U

umap_transform() (in module SlideMap) unclip() (in module Dataset) unwrap() (in module model.tensorflow)

update_annotations_with_slidenames() (in module Dataset) update_manifest() (in module Dataset) update_manifest_at_dir() (in module histox.io) update_results_log() (in module histox.util)

V

validate() (in module ModelParams) ValidJSONEncoder (class in histox.util) vanilla() (histox.grad.SaliencyMap method) verify_alignment() (in module WSI) verify_annotations_slides() (in module Dataset)

verify_img_format() (in module Dataset) verify_slide_names() (in module Dataset) view() (in module Heatmap) (in module Mosaic) (in module WSI)

W

write_json() (in module histox.util) write_tfrecords_merge() (in module histox.io)

write_tfrecords_multi() (in module histox.io) write_tfrecords_single() (in module histox.io) WSI (class in histox.slide)

X

xrai() (histox.grad.SaliencyMap method)

xrai_fast() (histox.grad.SaliencyMap method)

Y

yes_no_input() (in module histox.util)

Z

z() (histox.gan.StyleGAN2Interpolator method)