Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | Z _ __add__() (SQLExpression method) __mul__() (SQLExpression method) _ARRAY_DIMENSIONS (Zattrs attribute) _creator (Zattrs attribute) A active (Channel attribute) add_area_column() (SQLiteStore method) add_default_to_usage_help() (in module tiatoolbox.cli.common) add_from_dat() (in module tiatoolbox.utils.misc) add_from_geojson() (AnnotationStore method) add_layer() (in module tiatoolbox.visualization.bokeh_app.main) AffineWSITransformer (class in tiatoolbox.tools.registration.wsi_registration) affinity_to_edge_index() (in module tiatoolbox.tools.graph) Annotation (class in tiatoolbox.annotation.storage) AnnotationRenderer (class in tiatoolbox.utils.visualization) AnnotationStore (class in tiatoolbox.annotation.storage) AnnotationStoreReader (class in tiatoolbox.wsicore.wsireader) AnnotationTileGenerator (class in tiatoolbox.tools.pyramid) anns_from_hoverdict() (in module tiatoolbox.utils.misc) append() (AnnotationStore method) (DictionaryStore method) append_many() (AnnotationStore method) (SQLiteStore method) apply() (StainAugmentor method) apply_affine_transformation() (in module tiatoolbox.tools.registration.wsi_registration) apply_bspline_transform() (in module tiatoolbox.tools.registration.wsi_registration) ArrayView (class in tiatoolbox.wsicore.wsireader) as_dict() (WSIMeta method) assert_dtype_int() (in module tiatoolbox.utils.misc) augment() (StainAugmentor method) axes (Multiscales attribute) (WSIMeta attribute) Axis (class in tiatoolbox.wsicore.metadata.ngff) B background_composite() (in module tiatoolbox.utils.transforms) batch_size (PatchPredictor attribute) bind_cb_obj() (in module tiatoolbox.visualization.bokeh_app.main) bind_cb_obj_tog() (in module tiatoolbox.visualization.bokeh_app.main) blur_spinner_cb() (in module tiatoolbox.visualization.bokeh_app.main) bounds2locsize() (in module tiatoolbox.utils.transforms) bounds2slices() (in module tiatoolbox.utils.transforms) bquery() (AnnotationStore method) (SQLiteStore method) build() (SlideGraphConstructor static method) build_predicate() (in module tiatoolbox.visualization.bokeh_app.main) C centre_crop() (in module tiatoolbox.models.architecture.utils) centre_crop_to_shape() (in module tiatoolbox.models.architecture.utils) change_mapper() (TileServer method) change_overlay() (TileServer method) change_prop() (TileServer method) change_secondary_cmap() (TileServer method) change_slide() (TileServer method) change_tiles() (in module tiatoolbox.visualization.bokeh_app.main) Channel (class in tiatoolbox.wsicore.metadata.ngff) channels (Omero attribute) check_pixman_using_anaconda() (in module tiatoolbox.utils.env_detection) check_pixman_using_brew() (in module tiatoolbox.utils.env_detection) check_pixman_using_dpkg() (in module tiatoolbox.utils.env_detection) check_pixman_using_macports() (in module tiatoolbox.utils.env_detection) classifier (CNNModel attribute) clear() (AnnotationStore method) (SQLiteStore method) cli_auto_generate_mask() (in module tiatoolbox.cli.common) cli_batch_size() (in module tiatoolbox.cli.common) cli_file_type() (in module tiatoolbox.cli.common) cli_img_input() (in module tiatoolbox.cli.common) cli_masks() (in module tiatoolbox.cli.common) cli_merge_predictions() (in module tiatoolbox.cli.common) cli_method() (in module tiatoolbox.cli.common) cli_mode() (in module tiatoolbox.cli.common) cli_name() (in module tiatoolbox.cli.common) cli_num_loader_workers() (in module tiatoolbox.cli.common) cli_num_postproc_workers() (in module tiatoolbox.cli.common) cli_on_gpu() (in module tiatoolbox.cli.common) cli_output_path() (in module tiatoolbox.cli.common) cli_pretrained_model() (in module tiatoolbox.cli.common) cli_pretrained_weights() (in module tiatoolbox.cli.common) cli_region() (in module tiatoolbox.cli.common) cli_resolution() (in module tiatoolbox.cli.common) cli_return_labels() (in module tiatoolbox.cli.common) cli_return_probabilities() (in module tiatoolbox.cli.common) cli_tile_format() (in module tiatoolbox.cli.common) cli_tile_objective() (in module tiatoolbox.cli.common) cli_tile_read_size() (in module tiatoolbox.cli.common) cli_units() (in module tiatoolbox.cli.common) cli_verbose() (in module tiatoolbox.cli.common) cli_yaml_config_path() (in module tiatoolbox.cli.common) close() (DictionaryStore method) (SQLiteStore method) cmap_select_cb() (in module tiatoolbox.visualization.bokeh_app.main) CNNBackbone (class in tiatoolbox.models.architecture.vanilla) CNNModel (class in tiatoolbox.models.architecture.vanilla) colab_has_gpu() (in module tiatoolbox.utils.env_detection) collate_fn() (WSIStreamDataset static method) color (Channel attribute) color_input_cb() (in module tiatoolbox.visualization.bokeh_app.main) ColorCycler (class in tiatoolbox.visualization.bokeh_app.main) colourise_image() (in module tiatoolbox.utils.visualization) commit() (AnnotationStore method) (DictionaryStore method) (SQLiteStore method) commit_db() (TileServer method) compile_options() (SQLiteStore static method) compute_center_of_mass() (in module tiatoolbox.tools.registration.wsi_registration) compute_feature_distances() (DFBRegister static method) con (SQLiteMetadata attribute) contrast_enhancer() (in module tiatoolbox.utils.misc) control_tabs_cb() (in module tiatoolbox.visualization.bokeh_app.main) control_tabs_remove_cb() (in module tiatoolbox.visualization.bokeh_app.main) ConvBnRelu (class in tiatoolbox.models.architecture.nuclick) convert_resolution_units() (WSIReader method) coordinate_list (PatchExtractor attribute) CoordinateTransform (class in tiatoolbox.wsicore.metadata.ngff) coordinateTransformations (Dataset attribute) coords (Annotation property) cprop_input_cb() (in module tiatoolbox.visualization.bokeh_app.main) create_block() (in module tiatoolbox.models.architecture.unet) create_index() (SQLiteStore method) Creator (class in tiatoolbox.wsicore.metadata.ngff) crop_and_pad_edges() (in module tiatoolbox.utils.image) CustomExtractor (class in tiatoolbox.tools.stainextract) CustomNormalizer (class in tiatoolbox.tools.stainnorm) D Dataset (class in tiatoolbox.wsicore.metadata.ngff) DatasetInfoABC (class in tiatoolbox.models.dataset.info) datasets (Multiscales attribute) decode_safe_name() (TileServer static method) decode_wkb() (Annotation static method) DeepFeatureExtractor (class in tiatoolbox.models.engine.semantic_segmentor) defaultT (RDefs attribute) defaultZ (RDefs attribute) delaunay_adjacency() (in module tiatoolbox.tools.graph) DenseBlock (class in tiatoolbox.models.architecture.hovernet) deserialize_geometry() (AnnotationStore static method) (SQLiteStore method) DFBRegister (class in tiatoolbox.tools.registration.wsi_registration) DFBRFeatureExtractor (class in tiatoolbox.tools.registration.wsi_registration) dice() (in module tiatoolbox.utils.metrics) DICOMWSIReader (class in tiatoolbox.wsicore.wsireader) dict_to_store() (in module tiatoolbox.utils.misc) dict_to_zarr() (in module tiatoolbox.utils.misc) DictionaryStore (class in tiatoolbox.annotation.storage) dl_output_for_h_and_e() (in module tiatoolbox.tools.stainextract) DocConfig (class in tiatoolbox.visualization.bokeh_app.main) download_data() (in module tiatoolbox.utils.misc) drop_index() (SQLiteStore method) DummyAttr (class in tiatoolbox.visualization.bokeh_app.main) dump() (AnnotationStore method) (DictionaryStore method) (SQLiteStore method) (TilePyramidGenerator method) dumps() (AnnotationStore method) (DictionaryStore method) (SQLiteStore method) DuplicateFilter (class in tiatoolbox) E edge_index_to_triangles() (in module tiatoolbox.tools.graph) edge_size_cb() (in module tiatoolbox.visualization.bokeh_app.main) end (Window attribute) estimate_affine_transform() (DFBRegister static method) estimate_bspline_transform() (in module tiatoolbox.tools.registration.wsi_registration) extract_features() (DFBRegister method) extractor (StainNormalizer attribute) ExtractorParams (class in tiatoolbox.tools.patchextraction) F f1_detection() (in module tiatoolbox.utils.metrics) family (Channel attribute) feat_extract (CNNModel attribute) feature_mapping() (DFBRegister method) features() (AnnotationStore method) (SQLiteStore method) fetch_pretrained_weights() (in module tiatoolbox.models.architecture) file_path (WSIMeta attribute) FileNotSupportedError filter() (DuplicateFilter method) filter_coordinates() (PatchExtractor static method) (SemanticSegmentor static method) filter_input_cb() (in module tiatoolbox.visualization.bokeh_app.main) filtering_matching_points() (DFBRegister method) find_overlap() (in module tiatoolbox.utils.image) find_padding() (in module tiatoolbox.utils.image) find_points_inside_boundary() (DFBRegister static method) find_read_rect_params() (WSIReader method) finding_match() (DFBRegister static method) fit() (OtsuTissueMasker method) (ReinhardNormalizer method) (StainAugmentor method) (StainNormalizer method) (TissueMasker method) fit_transform() (TissueMasker method) fixed_layer_select_cb() (in module tiatoolbox.visualization.bokeh_app.main) format_info() (in module tiatoolbox.visualization.bokeh_app.main) forward() (CNNBackbone method) (CNNModel method) (ConvBnRelu method) (DenseBlock method) (DFBRFeatureExtractor method) (HoVerNet method) (MapDe method) (MicroNet method) (ModelABC method) (MultiscaleConvBlock method) (NuClick method) (ResidualBlock method) (ResidualConv method) (SCCNN method) (TFSamepaddingLayer method) (UnetEncoder method) (UNetModel method) (UpSample2x method) forward_hook() (DFBRFeatureExtractor method) from_dataframe() (AnnotationStore class method) from_geojson() (AnnotationStore class method) from_ndjson() (AnnotationStore class method) G gather_ui_elements() (in module tiatoolbox.visualization.bokeh_app.main) generate_random() (ColorCycler static method) geometry (Annotation attribute) (Annotation property) geometry_type (Annotation property) GeometryType (class in tiatoolbox.enums) get() (SQLJSONDictionary method) get_ann_layer() (TileServer method) get_annotations() (TileServer method) get_block() (ConvBnRelu static method) get_bounding_box() (in module tiatoolbox.utils.misc) get_color() (AnnotationRenderer method) get_color_prop() (TileServer method) get_concentrations() (StainNormalizer static method) get_connection() (SQLiteStore method) get_coordinates() (PatchExtractor static method) (SemanticSegmentor static method) get_from_config() (in module tiatoolbox.visualization.bokeh_app.main) get_grp() (TileGroup method) get_instance_info() (HoVerNet static method) get_level_by_extent() (in module tiatoolbox.visualization.ui_utils) get_luminosity_tissue_mask() (in module tiatoolbox.utils.misc) get_mapper() (TileServer method) get_mapper_for_prop() (in module tiatoolbox.visualization.bokeh_app.main) get_mean_std() (ReinhardNormalizer method) get_next() (ColorCycler method) get_normalizer() (in module tiatoolbox.tools.stainnorm) get_overlay() (TileServer method) get_params() (StainAugmentor method) get_params_dependent_on_targets() (StainAugmentor method) get_patch_dimensions() (AffineWSITransformer method) get_patch_extractor() (in module tiatoolbox.tools.patchextraction) get_pretrained_model() (in module tiatoolbox.models.architecture) get_properties() (TileServer method) get_property_values() (TileServer method) get_random() (ColorCycler method) get_reader() (SemanticSegmentor static method) get_renderer() (TileServer method) get_secondary_cmap() (TileServer method) get_slide() (TileServer method) get_stain_matrix() (CustomExtractor method) (MacenkoExtractor method) (RuifrokExtractor method) (VahadaneExtractor method) get_thumb_tile() (AnnotationTileGenerator method) (TilePyramidGenerator method) get_tile() (AnnotationTileGenerator method) (TilePyramidGenerator method) get_tissue_regions() (DFBRegister static method) get_transform_init_args_names() (StainAugmentor static method) get_transformed_location() (AffineWSITransformer method) get_view_bounds() (in module tiatoolbox.visualization.bokeh_app.main) glymur_wsi (JP2WSIReader attribute) grab_files_from_dir() (in module tiatoolbox.utils.misc) group1_arch_branch() (in module tiatoolbox.models.architecture.micronet) group1_forward_branch() (in module tiatoolbox.models.architecture.micronet) group2_arch_branch() (in module tiatoolbox.models.architecture.micronet) group2_forward_branch() (in module tiatoolbox.models.architecture.micronet) group3_arch_branch() (in module tiatoolbox.models.architecture.micronet) group3_forward_branch() (in module tiatoolbox.models.architecture.micronet) group4_arch_branch() (in module tiatoolbox.models.architecture.micronet) group4_forward_branch() (in module tiatoolbox.models.architecture.micronet) H h_and_e_in_right_order() (in module tiatoolbox.tools.stainextract) handle_graph_layer() (in module tiatoolbox.visualization.bokeh_app.main) has_gpu() (in module tiatoolbox.utils.env_detection) has_network() (in module tiatoolbox.utils.env_detection) hex2rgb() (in module tiatoolbox.visualization.bokeh_app.main) HoVerNet (class in tiatoolbox.models.architecture.hovernet) HoVerNetPlus (class in tiatoolbox.models.architecture.hovernetplus) I id (Omero attribute) IDaRS (class in tiatoolbox.models.architecture.idars) img (PatchPredictor attribute) (VirtualWSIReader attribute) imread() (in module tiatoolbox.utils.misc) imresize() (in module tiatoolbox.utils.transforms) imwrite() (in module tiatoolbox.utils.misc) in_conda_env() (in module tiatoolbox.utils.env_detection) index() (TileServer method) indexes() (SQLiteStore method) infer_batch() (CNNBackbone static method) (CNNModel static method) (HoVerNet static method) (HoVerNetPlus static method) (MapDe static method) (MicroNet static method) (ModelABC static method) (NuClick static method) (SCCNN static method) (UNetModel static method) info (WSIReader property) initialise_overlay() (in module tiatoolbox.visualization.bokeh_app.main) initialise_slide() (in module tiatoolbox.visualization.bokeh_app.main) input_path (WSIReader attribute) input_resolutions (IOConfigABC property) inputs (DatasetInfoABC property) (KatherPatchDataset attribute) (PatchDataset attribute) (WSIPatchDataset attribute) inverted (Channel attribute) IOConfigABC (class in tiatoolbox.models.models_abc) IOPatchPredictorConfig (class in tiatoolbox.models.engine.patch_predictor) IOSegmentorConfig (class in tiatoolbox.models.engine.semantic_segmentor) iquery() (AnnotationStore method) (SQLiteStore method) is_dcm() (in module tiatoolbox.utils.magic) is_dicom() (in module tiatoolbox.wsicore.wsireader) is_dir() (in module tiatoolbox.utils.magic) is_interactive() (in module tiatoolbox.utils.env_detection) is_ngff() (in module tiatoolbox.wsicore.wsireader) is_notebook() (in module tiatoolbox.utils.env_detection) is_sqlite3() (in module tiatoolbox.utils.magic) is_tiled_tiff() (in module tiatoolbox.wsicore.wsireader) is_zarr() (in module tiatoolbox.wsicore.wsireader) is_zip() (in module tiatoolbox.utils.magic) items() (DictionaryStore method) (SQLiteStore method) J JP2WSIReader (class in tiatoolbox.wsicore.wsireader) json_contains() (in module tiatoolbox.annotation.dsl) json_list_sum() (in module tiatoolbox.annotation.dsl) K KatherPatchDataset (class in tiatoolbox.models.dataset.info) keys() (AnnotationStore method) (SQLiteStore method) L lab_split() (ReinhardNormalizer static method) label_names (DatasetInfoABC property) (KatherPatchDataset attribute) labels (DatasetInfoABC property) (KatherPatchDataset attribute) (PatchDataset attribute) layer_drop_cb() (in module tiatoolbox.visualization.bokeh_app.main) layer_select_cb() (in module tiatoolbox.visualization.bokeh_app.main) layer_slider_cb() (in module tiatoolbox.visualization.bokeh_app.main) level_count (AnnotationTileGenerator property) (TilePyramidGenerator property) (WSIMeta attribute) level_dimensions (WSIMeta attribute) level_dimensions() (AnnotationTileGenerator method) (TilePyramidGenerator method) level_downsample() (TilePyramidGenerator method) (WSIMeta method) level_downsamples (WSIMeta attribute) lhs (SQLTriplet attribute) load_annotations() (TileServer method) load_img() (PatchDatasetABC static method) load_stain_matrix() (in module tiatoolbox.utils.misc) load_weights_from_file() (ModelABC method) locations_df (PatchExtractor attribute) locsize2bounds() (in module tiatoolbox.utils.transforms) M MacenkoExtractor (class in tiatoolbox.tools.stainextract) MacenkoNormalizer (class in tiatoolbox.tools.stainnorm) make_bounds_size_positive() (in module tiatoolbox.utils.image) make_color_dict() (in module tiatoolbox.visualization.bokeh_app.main) make_color_seq_from_cmap() (in module tiatoolbox.visualization.bokeh_app.main) make_default_dict() (in module tiatoolbox.utils.misc) make_safe_name() (in module tiatoolbox.visualization.bokeh_app.main) make_ts() (in module tiatoolbox.visualization.bokeh_app.main) make_valid_poly() (in module tiatoolbox.utils.misc) make_window() (in module tiatoolbox.visualization.bokeh_app.main) MapDe (class in tiatoolbox.models.architecture.mapde) match_histograms() (in module tiatoolbox.tools.registration.wsi_registration) max (Window attribute) maxC_target (StainNormalizer attribute) merge_back() (ReinhardNormalizer static method) merge_prediction() (SemanticSegmentor static method) merge_predictions() (PatchPredictor static method) MethodNotSupportedError MicroNet (class in tiatoolbox.models.architecture.micronet) min (Window attribute) min_mask_ratio (PatchExtractor attribute) mode (PatchPredictor attribute) (VirtualWSIReader attribute) model (PatchPredictor attribute) (RDefs attribute) model_drop_cb() (in module tiatoolbox.visualization.bokeh_app.main) model_to() (in module tiatoolbox.utils.misc) ModelABC (class in tiatoolbox.models.models_abc) module tiatoolbox tiatoolbox.annotation tiatoolbox.annotation.dsl tiatoolbox.annotation.storage tiatoolbox.cli tiatoolbox.cli.common tiatoolbox.cli.nucleus_instance_segment tiatoolbox.cli.patch_predictor tiatoolbox.cli.read_bounds tiatoolbox.cli.save_tiles tiatoolbox.cli.semantic_segment tiatoolbox.cli.show_wsi tiatoolbox.cli.slide_info tiatoolbox.cli.slide_thumbnail tiatoolbox.cli.stain_norm tiatoolbox.cli.tissue_mask tiatoolbox.cli.visualize tiatoolbox.data tiatoolbox.enums tiatoolbox.models tiatoolbox.models.architecture tiatoolbox.models.architecture.hovernet tiatoolbox.models.architecture.hovernetplus tiatoolbox.models.architecture.idars tiatoolbox.models.architecture.mapde tiatoolbox.models.architecture.micronet tiatoolbox.models.architecture.nuclick tiatoolbox.models.architecture.sccnn tiatoolbox.models.architecture.unet tiatoolbox.models.architecture.utils tiatoolbox.models.architecture.vanilla tiatoolbox.models.dataset tiatoolbox.models.dataset.classification tiatoolbox.models.dataset.dataset_abc tiatoolbox.models.dataset.info tiatoolbox.models.engine tiatoolbox.models.engine.multi_task_segmentor tiatoolbox.models.engine.nucleus_instance_segmentor tiatoolbox.models.engine.patch_predictor tiatoolbox.models.engine.semantic_segmentor tiatoolbox.models.models_abc tiatoolbox.tiatoolbox tiatoolbox.tools tiatoolbox.tools.graph tiatoolbox.tools.patchextraction tiatoolbox.tools.pyramid tiatoolbox.tools.registration tiatoolbox.tools.registration.wsi_registration tiatoolbox.tools.stainaugment tiatoolbox.tools.stainextract tiatoolbox.tools.stainnorm tiatoolbox.tools.tissuemask tiatoolbox.typing tiatoolbox.utils tiatoolbox.utils.env_detection tiatoolbox.utils.exceptions tiatoolbox.utils.image tiatoolbox.utils.magic tiatoolbox.utils.metrics tiatoolbox.utils.misc tiatoolbox.utils.transforms tiatoolbox.utils.visualization tiatoolbox.visualization tiatoolbox.visualization.bokeh_app tiatoolbox.visualization.bokeh_app.app_hooks tiatoolbox.visualization.bokeh_app.main tiatoolbox.visualization.tileserver tiatoolbox.visualization.ui_utils tiatoolbox.wsicore tiatoolbox.wsicore.metadata tiatoolbox.wsicore.metadata.ngff tiatoolbox.wsicore.wsimeta tiatoolbox.wsicore.wsireader MorphologicalMasker (class in tiatoolbox.tools.tissuemask) mpp (WSIMeta attribute) MultiscaleConvBlock (class in tiatoolbox.models.architecture.nuclick) Multiscales (class in tiatoolbox.wsicore.metadata.ngff) multiscales (Zattrs attribute) MultiTaskSegmentor (class in tiatoolbox.models.engine.multi_task_segmentor) N n (PatchExtractor attribute) n_stains (StainAugmentor attribute) name (Axis attribute) (Creator attribute) (Omero attribute) name2type() (in module tiatoolbox.visualization.bokeh_app.main) NGFFWSIReader (class in tiatoolbox.wsicore.wsireader) no_input_message() (in module tiatoolbox.cli.common) node_select_cb() (in module tiatoolbox.visualization.bokeh_app.main) normalize_padding_size() (in module tiatoolbox.utils.image) nquery() (AnnotationStore method) NucleusInstanceSegmentor (class in tiatoolbox.models.engine.nucleus_instance_segmentor) NuClick (class in tiatoolbox.models.architecture.nuclick) num_classes (CNNModel attribute) num_loader_worker (PatchPredictor attribute) O objective_power (WSIMeta attribute) od2rgb() (in module tiatoolbox.utils.transforms) Omero (class in tiatoolbox.wsicore.metadata.ngff) omero (Zattrs attribute) on_session_destroyed() (in module tiatoolbox.visualization.bokeh_app.app_hooks) op (SQLTriplet attribute) open() (AnnotationStore class method) (DictionaryStore class method) (SQLiteStore class method) (WSIReader static method) openslide_wsi (OpenSlideWSIReader attribute) OpenSlideWSIReader (class in tiatoolbox.wsicore.wsireader) opt_buttons_cb() (in module tiatoolbox.visualization.bokeh_app.main) optimize() (SQLiteStore method) OtsuTissueMasker (class in tiatoolbox.tools.tissuemask) out_arch_branch() (in module tiatoolbox.models.architecture.micronet) output_resolutions (IOConfigABC property) output_tile_size (TilePyramidGenerator property) overlay_alpha_cb() (in module tiatoolbox.visualization.bokeh_app.main) overlay_prediction_contours() (in module tiatoolbox.utils.visualization) overlay_prediction_mask() (in module tiatoolbox.utils.visualization) overlay_probability_map() (in module tiatoolbox.utils.visualization) overlay_toggle_cb() (in module tiatoolbox.visualization.bokeh_app.main) P pad_bounds() (in module tiatoolbox.utils.transforms) pad_constant_values (PatchExtractor attribute) pad_mode (PatchExtractor attribute) PADDING_TO_BOUNDS (in module tiatoolbox.utils.image) pair_coordinates() (in module tiatoolbox.utils.metrics) parse_cv2_interpolaton() (in module tiatoolbox.utils.misc) patch() (AnnotationStore method) (DictionaryStore method) patch_input_shape (WSIPatchDataset attribute) patch_many() (AnnotationStore method) (SQLiteStore method) patch_size (PatchExtractor attribute) PatchDataset (class in tiatoolbox.models.dataset.classification) PatchDatasetABC (class in tiatoolbox.models.dataset.dataset_abc) PatchExtractor (class in tiatoolbox.tools.patchextraction) PatchExtractorABC (class in tiatoolbox.tools.patchextraction) PatchPredictor (class in tiatoolbox.models.engine.patch_predictor) path (Dataset attribute) perform_dfbregister() (DFBRegister method) perform_dfbregister_block_wise() (DFBRegister method) pixman_versions() (in module tiatoolbox.utils.env_detection) pixman_warning() (in module tiatoolbox.utils.env_detection) plot_graph() (in module tiatoolbox.utils.visualization) PointsPatchExtractor (class in tiatoolbox.tools.patchextraction) PointsPatchExtractorParams (class in tiatoolbox.tools.patchextraction) pool (CNNModel attribute) populate_layer_list() (in module tiatoolbox.visualization.bokeh_app.main) populate_slide_list() (in module tiatoolbox.visualization.bokeh_app.main) postproc() (CNNModel static method) (HoVerNet static method) (HoVerNetPlus static method) (MapDe method) (MicroNet static method) (ModelABC static method) (NuClick static method) (SCCNN method) postproc_func (ModelABC property) ppu2mpp() (in module tiatoolbox.utils.misc) pquery() (AnnotationStore method) (SQLiteStore method) prealignment() (in module tiatoolbox.tools.registration.wsi_registration) predefined_preproc_func() (in module tiatoolbox.models.dataset.classification) predict() (DeepFeatureExtractor method) (PatchPredictor method) (SemanticSegmentor method) prepare_file_dir_cli() (in module tiatoolbox.cli.common) prepare_ioconfig_seg() (in module tiatoolbox.cli.common) prepare_model_cli() (in module tiatoolbox.cli.common) preproc() (IDaRS static method) (MicroNet static method) (ModelABC static method) (PatchDatasetABC static method) (SCCNN static method) preproc_func (ModelABC property) (PatchDatasetABC property) (WSIPatchDataset attribute) pretrained_model (PatchPredictor attribute) process_prediction_per_batch (SemanticSegmentor attribute) prop_range() (TileServer method) properties (Annotation attribute) pt_size_cb() (in module tiatoolbox.visualization.bokeh_app.main) py_is_none() (in module tiatoolbox.annotation.dsl) py_is_not_none() (in module tiatoolbox.annotation.dsl) py_regexp() (in module tiatoolbox.annotation.dsl) Q query() (AnnotationStore method) (SQLiteStore method) R random_colors() (in module tiatoolbox.utils.visualization) raw (WSIMeta attribute) RDefs (class in tiatoolbox.wsicore.metadata.ngff) rdefs (Omero attribute) read_bounds() (AnnotationStoreReader method) (DICOMWSIReader method) (JP2WSIReader method) (NGFFWSIReader method) (OpenSlideWSIReader method) (TIFFWSIReader method) (VirtualWSIReader method) (WSIReader method) read_locations() (in module tiatoolbox.utils.misc) read_rect() (AffineWSITransformer method) (AnnotationStoreReader method) (DICOMWSIReader method) (JP2WSIReader method) (NGFFWSIReader method) (OpenSlideWSIReader method) (TIFFWSIReader method) (VirtualWSIReader method) (WSIReader method) read_region() (WSIReader method) read_registry_files() (in module tiatoolbox) reader (WSIPatchDataset attribute) register() (DFBRegister method) ReinhardNormalizer (class in tiatoolbox.tools.stainnorm) relative_level_scales() (WSIMeta method) remove() (AnnotationStore method) (DictionaryStore method) remove_area_column() (SQLiteStore method) remove_many() (AnnotationStore method) (SQLiteStore method) render_annotations() (AnnotationRenderer method) render_by_type() (AnnotationRenderer method) render_line() (AnnotationRenderer method) render_multipoly() (AnnotationRenderer method) render_poly() (AnnotationRenderer method) render_pt() (AnnotationRenderer method) res_switch_cb() (in module tiatoolbox.visualization.bokeh_app.main) reset() (TileServer method) ResidualBlock (class in tiatoolbox.models.architecture.hovernet) ResidualConv (class in tiatoolbox.models.architecture.nuclick) resnet() (ResNetEncoder static method) resnet50() (ResNetEncoder static method) ResNetEncoder (class in tiatoolbox.models.architecture.unet) resolution (PatchExtractor attribute) (WSIPatchDataset attribute) rgb2hex() (in module tiatoolbox.visualization.bokeh_app.main) rgb2od() (in module tiatoolbox.utils.transforms) rhs (SQLTriplet attribute) RuifrokExtractor (class in tiatoolbox.tools.stainextract) RuifrokNormalizer (class in tiatoolbox.tools.stainnorm) running_on_ci() (in module tiatoolbox.utils.env_detection) running_on_circleci() (in module tiatoolbox.utils.env_detection) running_on_colab() (in module tiatoolbox.utils.env_detection) running_on_github() (in module tiatoolbox.utils.env_detection) running_on_kaggle() (in module tiatoolbox.utils.env_detection) running_on_travis() (in module tiatoolbox.utils.env_detection) S safe_padded_read() (in module tiatoolbox.utils.image) save_as_json() (in module tiatoolbox.utils.misc) save_cb() (in module tiatoolbox.visualization.bokeh_app.main) save_tiles() (WSIReader method) save_yaml() (in module tiatoolbox.utils.misc) scale (CoordinateTransform attribute) scale_spinner_cb() (in module tiatoolbox.visualization.bokeh_app.main) scale_to_highest() (IOSegmentorConfig static method) SCCNN (class in tiatoolbox.models.architecture.sccnn) search() (SQLRegex class method) segment_on_box() (in module tiatoolbox.visualization.bokeh_app.main) select_cv2_interpolation() (in module tiatoolbox.utils.misc) select_device() (in module tiatoolbox.utils.misc) SemanticSegmentor (class in tiatoolbox.models.engine.semantic_segmentor) serialise_geometry() (AnnotationStore static method) (SQLiteStore method) session_id() (TileServer method) set_alpha_glyph() (in module tiatoolbox.visualization.bokeh_app.main) set_sys_args() (DocConfig method) setdefault() (AnnotationStore method) setup_config_ui_settings() (in module tiatoolbox.visualization.bokeh_app.main) setup_doc() (DocConfig method) shape (ArrayView property) shutdown() (TileServer static method) slide_alpha_cb() (in module tiatoolbox.visualization.bokeh_app.main) slide_dimensions (WSIMeta attribute) slide_dimensions() (WSIReader method) slide_select_cb() (in module tiatoolbox.visualization.bokeh_app.main) slide_thumbnail() (WSIReader method) slide_toggle_cb() (in module tiatoolbox.visualization.bokeh_app.main) SlideGraphConstructor (class in tiatoolbox.tools.graph) SlidingWindowPatchExtractor (class in tiatoolbox.tools.patchextraction) SlidingWindowPatchExtractorParams (class in tiatoolbox.tools.patchextraction) small_svs() (in module tiatoolbox.data) source_concentrations (StainAugmentor attribute) spatially_constrained_layer2() (SCCNN method) split_path_name_ext() (in module tiatoolbox.utils.misc) sql_has_key() (in module tiatoolbox.annotation.dsl) sql_is_none() (in module tiatoolbox.annotation.dsl) sql_is_not_none() (in module tiatoolbox.annotation.dsl) sql_list_sum() (in module tiatoolbox.annotation.dsl) SQLExpression (class in tiatoolbox.annotation.dsl) SQLiteMetadata (class in tiatoolbox.annotation.storage) SQLiteStore (class in tiatoolbox.annotation.storage) SQLJSONDictionary (class in tiatoolbox.annotation.dsl) SQLNone (class in tiatoolbox.annotation.dsl) SQLRegex (class in tiatoolbox.annotation.dsl) SQLTriplet (class in tiatoolbox.annotation.dsl) stain_matrix (StainAugmentor attribute) stain_matrix_target (StainNormalizer attribute) stain_matrix_target_RGB (StainNormalizer attribute) stain_norm_target() (in module tiatoolbox.data) stain_normalizer (StainAugmentor attribute) StainAugmentor (class in tiatoolbox.tools.stainaugment) StainNormalizer (class in tiatoolbox.tools.stainnorm) start (Window attribute) store_from_dat() (in module tiatoolbox.utils.misc) stride (PatchExtractor attribute) (SlidingWindowPatchExtractor attribute) string_to_tuple() (in module tiatoolbox.utils.misc) sub_pixel_read() (in module tiatoolbox.utils.image) sub_tile_level_count (TilePyramidGenerator property) T tap_event_cb() (in module tiatoolbox.visualization.bokeh_app.main) tap_query() (TileServer method) target_concentrations (StainNormalizer attribute) target_means (ReinhardNormalizer attribute) target_stds (ReinhardNormalizer attribute) TFSamepaddingLayer (class in tiatoolbox.models.architecture.hovernet) tiatoolbox module tiatoolbox.annotation module tiatoolbox.annotation.dsl module tiatoolbox.annotation.storage module tiatoolbox.cli module tiatoolbox.cli.common module tiatoolbox.cli.nucleus_instance_segment module tiatoolbox.cli.patch_predictor module tiatoolbox.cli.read_bounds module tiatoolbox.cli.save_tiles module tiatoolbox.cli.semantic_segment module tiatoolbox.cli.show_wsi module tiatoolbox.cli.slide_info module tiatoolbox.cli.slide_thumbnail module tiatoolbox.cli.stain_norm module tiatoolbox.cli.tissue_mask module tiatoolbox.cli.visualize module tiatoolbox.data module tiatoolbox.enums module tiatoolbox.models module tiatoolbox.models.architecture module tiatoolbox.models.architecture.hovernet module tiatoolbox.models.architecture.hovernetplus module tiatoolbox.models.architecture.idars module tiatoolbox.models.architecture.mapde module tiatoolbox.models.architecture.micronet module tiatoolbox.models.architecture.nuclick module tiatoolbox.models.architecture.sccnn module tiatoolbox.models.architecture.unet module tiatoolbox.models.architecture.utils module tiatoolbox.models.architecture.vanilla module tiatoolbox.models.dataset module tiatoolbox.models.dataset.classification module tiatoolbox.models.dataset.dataset_abc module tiatoolbox.models.dataset.info module tiatoolbox.models.engine module tiatoolbox.models.engine.multi_task_segmentor module tiatoolbox.models.engine.nucleus_instance_segmentor module tiatoolbox.models.engine.patch_predictor module tiatoolbox.models.engine.semantic_segmentor module tiatoolbox.models.models_abc module tiatoolbox.tiatoolbox module tiatoolbox.tools module tiatoolbox.tools.graph module tiatoolbox.tools.patchextraction module tiatoolbox.tools.pyramid module tiatoolbox.tools.registration module tiatoolbox.tools.registration.wsi_registration module tiatoolbox.tools.stainaugment module tiatoolbox.tools.stainextract module tiatoolbox.tools.stainnorm module tiatoolbox.tools.tissuemask module tiatoolbox.typing module tiatoolbox.utils module tiatoolbox.utils.env_detection module tiatoolbox.utils.exceptions module tiatoolbox.utils.image module tiatoolbox.utils.magic module tiatoolbox.utils.metrics module tiatoolbox.utils.misc module tiatoolbox.utils.transforms module tiatoolbox.utils.visualization module tiatoolbox.visualization module tiatoolbox.visualization.bokeh_app module tiatoolbox.visualization.bokeh_app.app_hooks module tiatoolbox.visualization.bokeh_app.main module tiatoolbox.visualization.tileserver module tiatoolbox.visualization.ui_utils module tiatoolbox.wsicore module tiatoolbox.wsicore.metadata module tiatoolbox.wsicore.metadata.ngff module tiatoolbox.wsicore.wsimeta module tiatoolbox.wsicore.wsireader module TIAToolboxCLI (class in tiatoolbox.cli.common) TIFFWSIReader (class in tiatoolbox.wsicore.wsireader) tile_grid_size() (TilePyramidGenerator method) tile_group() (ZoomifyGenerator method) tile_path() (TilePyramidGenerator method) (ZoomifyGenerator method) TileGroup (class in tiatoolbox.visualization.bokeh_app.main) TilePyramidGenerator (class in tiatoolbox.tools.pyramid) TileServer (class in tiatoolbox.visualization.tileserver) tissue_mask (StainAugmentor attribute) tissue_mask() (WSIReader method) TissueMasker (class in tiatoolbox.tools.tissuemask) to() (ModelABC method) to_baseline() (IOSegmentorConfig method) to_dataframe() (AnnotationStore method) (SQLiteStore method) to_feature() (Annotation method) to_float_rgb() (in module tiatoolbox.visualization.bokeh_app.main) to_geodict() (AnnotationStore method) to_geojson() (Annotation method) (AnnotationStore method) to_int_rgb() (in module tiatoolbox.visualization.bokeh_app.main) to_model_cb() (in module tiatoolbox.visualization.bokeh_app.main) to_ndjson() (AnnotationStore method) to_num() (in module tiatoolbox.visualization.bokeh_app.main) to_tile_coords() (AnnotationRenderer static method) to_wkb() (Annotation method) to_wkt() (Annotation method) transform() (AnnotationStore method) (MorphologicalMasker method) (OtsuTissueMasker method) (ReinhardNormalizer method) (StainNormalizer method) (TissueMasker method) transform_patch() (AffineWSITransformer method) transform_points() (AffineWSITransformer static method) triangle_signed_area() (in module tiatoolbox.tools.graph) type (Axis attribute) (CoordinateTransform attribute) type_cmap_cb() (in module tiatoolbox.visualization.bokeh_app.main) U UIWrapper (class in tiatoolbox.visualization.bokeh_app.main) UnetEncoder (class in tiatoolbox.models.architecture.unet) UNetModel (class in tiatoolbox.models.architecture.unet) unit (Axis attribute) units (PatchExtractor attribute) (WSIPatchDataset attribute) unzip_data() (in module tiatoolbox.utils.misc) update() (in module tiatoolbox.visualization.bokeh_app.main) update_mapper() (in module tiatoolbox.visualization.bokeh_app.main) update_renderer() (in module tiatoolbox.visualization.bokeh_app.main) (TileServer method) update_types() (TileServer static method) update_ui_on_new_annotations() (in module tiatoolbox.visualization.bokeh_app.main) UpSample2x (class in tiatoolbox.models.architecture.utils) V VahadaneExtractor (class in tiatoolbox.tools.stainextract) VahadaneNormalizer (class in tiatoolbox.tools.stainnorm) validate() (WSIMeta method) validate_shape() (in module tiatoolbox.tools.patchextraction) values() (AnnotationStore method) (SQLiteStore method) vectors_in_correct_direction() (in module tiatoolbox.tools.stainextract) vendor (WSIMeta attribute) verbose (PatchPredictor attribute) verify_supported_wsi() (WSIReader static method) version (Creator attribute) (Multiscales attribute) (Omero attribute) version_msg() (in module tiatoolbox.cli) version_to_tuple() (in module tiatoolbox.utils.env_detection) ViewerState (class in tiatoolbox.visualization.bokeh_app.main) VirtualWSIReader (class in tiatoolbox.wsicore.wsireader) visualise() (SlideGraphConstructor class method) W window (Channel attribute) Window (class in tiatoolbox.wsicore.metadata.ngff) wkb (Annotation attribute) (Annotation property) wsi (PatchExtractor attribute) WSIMeta (class in tiatoolbox.wsicore.wsimeta) WSIPatchDataset (class in tiatoolbox.models.dataset.classification) WSIReader (class in tiatoolbox.wsicore.wsireader) WSIStreamDataset (class in tiatoolbox.models.engine.semantic_segmentor) Z Zattrs (class in tiatoolbox.wsicore.metadata.ngff) zoomify() (TileServer method) ZoomifyGenerator (class in tiatoolbox.tools.pyramid)