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 _ _ARRAY_DIMENSIONS (Zattrs attribute) A 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) 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) append_many() (AnnotationStore method) (SQLiteStore method) apply() (StainAugmentor method) 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 (WSIMeta attribute) Axis (class in tiatoolbox.wsicore.metadata.ngff) B background_composite() (in module tiatoolbox.utils.transforms) batch_size (PatchPredictor attribute) bounds2locsize() (in module tiatoolbox.utils.transforms) bounds2slices() (in module tiatoolbox.utils.transforms) bquery() (AnnotationStore method) (SQLiteStore method) build() (SlideGraphConstructor static method) C centre_crop() (in module tiatoolbox.models.architecture.utils) centre_crop_to_shape() (in module tiatoolbox.models.architecture.utils) Channel (class in tiatoolbox.wsicore.metadata.ngff) channels (Omero attribute) 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_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() (SQLiteStore method) 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) colourise_image() (in module tiatoolbox.utils.visualization) commit() (AnnotationStore 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) connection (SQLiteMetadata attribute) contrast_enhancer() (in module tiatoolbox.utils.misc) 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) 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) DeepFeatureExtractor (class in tiatoolbox.models.engine.semantic_segmentor) 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) DictionaryStore (class in tiatoolbox.annotation.storage) dl_output_for_h_and_e() (in module tiatoolbox.tools.stainextract) download_data() (in module tiatoolbox.utils.misc) drop_index() (SQLiteStore method) dump() (AnnotationStore method) (TilePyramidGenerator method) dumps() (AnnotationStore method) E edge_index_to_triangles() (in module tiatoolbox.tools.graph) estimate_affine_transform() (DFBRegister static method) estimate_bspline_transform() (in module tiatoolbox.tools.registration.wsi_registration) extract_features() (DFBRegister method) extractor (StainNormalizer attribute) 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) FileNotSupported filter_coordinates() (PatchExtractor static method) (SemanticSegmentor static method) filter_coordinates_fast() (PatchExtractor static method) 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) 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 geometry (Annotation attribute) get() (SQLJSONDictionary method) get_block() (ConvBnRelu static method) get_bounding_box() (in module tiatoolbox.utils.misc) get_color() (AnnotationRenderer method) get_concentrations() (StainNormalizer static method) get_coordinates() (PatchExtractor static method) (SemanticSegmentor static method) get_instance_info() (HoVerNet static method) get_luminosity_tissue_mask() (in module tiatoolbox.utils.misc) get_mean_std() (ReinhardNormalizer method) get_normalizer() (in module tiatoolbox.tools.stainnorm) 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_reader() (SemanticSegmentor static 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 method) get_transformed_location() (AffineWSITransformer method) glymur_wsi (OmnyxJP2WSIReader 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) has_gpu() (in module tiatoolbox.utils.env_detection) has_network() (in module tiatoolbox.utils.env_detection) 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) input_path (WSIReader attribute) inputs (DatasetInfoABC attribute) (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_dicom() (in module tiatoolbox.wsicore.wsireader) is_interactive() (in module tiatoolbox.utils.env_detection) is_ngff() (in module tiatoolbox.wsicore.wsireader) is_notebook() (in module tiatoolbox.utils.env_detection) is_tiled_tiff() (in module tiatoolbox.wsicore.wsireader) is_zarr() (in module tiatoolbox.wsicore.wsireader) items() (DictionaryStore method) (SQLiteStore method) J 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 attribute) (KatherPatchDataset attribute) labels (KatherPatchDataset attribute) (PatchDataset attribute) 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_img() (PatchDatasetABC static method) load_stain_matrix() (in module tiatoolbox.utils.misc) 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_default_dict() (in module tiatoolbox.utils.misc) make_valid_poly() (in module tiatoolbox.utils.misc) 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) MethodNotSupported 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_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.data 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.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.utils tiatoolbox.utils.env_detection tiatoolbox.utils.exceptions tiatoolbox.utils.image tiatoolbox.utils.metrics tiatoolbox.utils.misc tiatoolbox.utils.transforms tiatoolbox.utils.visualization tiatoolbox.visualization tiatoolbox.visualization.tileserver tiatoolbox.wsicore tiatoolbox.wsicore.metadata tiatoolbox.wsicore.metadata.ngff tiatoolbox.wsicore.save_tiles tiatoolbox.wsicore.slide_info 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) N n (PatchExtractor attribute) n_stains (StainAugmentor attribute) NGFFWSIReader (class in tiatoolbox.wsicore.wsireader) no_input_message() (in module tiatoolbox.cli.common) normalize_padding_size() (in module tiatoolbox.utils.image) NucleusInstanceSegmentor (class in tiatoolbox.models.engine.nucleus_instance_segmentor) NuClick (class in tiatoolbox.models.architecture.nuclick) num_classes (CNNModel attribute) num_loader_workers (PatchPredictor attribute) O objective_power (WSIMeta attribute) od2rgb() (in module tiatoolbox.utils.transforms) Omero (class in tiatoolbox.wsicore.metadata.ngff) omero (Zattrs attribute) OmnyxJP2WSIReader (class in tiatoolbox.wsicore.wsireader) op (SQLTriplet attribute) open() (AnnotationStore class method) (SQLiteStore class method) (WSIReader static method) openslide_wsi (OpenSlideWSIReader attribute) OpenSlideWSIReader (class in tiatoolbox.wsicore.wsireader) optimize() (SQLiteStore method) OtsuTissueMasker (class in tiatoolbox.tools.tissuemask) out_arch_branch() (in module tiatoolbox.models.architecture.micronet) output_tile_size (TilePyramidGenerator property) overlay_prediction_contours() (in module tiatoolbox.utils.visualization) overlay_prediction_mask() (in module tiatoolbox.utils.visualization) overlay_probability_map() (in module tiatoolbox.utils.visualization) 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) 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 (SQLiteMetadata 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) pool (CNNModel attribute) 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) (PatchDataset attribute) (PatchDatasetABC property) (WSIPatchDataset attribute) pretrained_model (PatchPredictor attribute) process_prediction_per_batch (SemanticSegmentor attribute) properties (Annotation attribute) 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) (OmnyxJP2WSIReader method) (OpenSlideWSIReader method) (TIFFWSIReader method) (VirtualWSIReader method) (WSIReader method) read_locations() (in module tiatoolbox.utils.misc) read_rect() (AffineWSITransformer method) (AnnotationStoreReader method) (DICOMWSIReader method) (OmnyxJP2WSIReader method) (OpenSlideWSIReader method) (TIFFWSIReader method) (VirtualWSIReader method) (WSIReader method) read_region() (WSIReader method) reader (WSIPatchDataset attribute) register() (DFBRegister method) ReinhardNormalizer (class in tiatoolbox.tools.stainnorm) relative_level_scales() (WSIMeta method) remove() (AnnotationStore 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) 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) 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_tiles() (in module tiatoolbox.wsicore.save_tiles) (WSIReader method) save_yaml() (in module tiatoolbox.utils.misc) scale (CoordinateTransform attribute) scale_to_highest() (IOSegmentorConfig static method) SCCNN (class in tiatoolbox.models.architecture.sccnn) search() (SQLRegex class method) 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) setdefault() (AnnotationStore method) slide_dimensions (WSIMeta attribute) slide_dimensions() (WSIReader method) slide_info() (in module tiatoolbox.wsicore.slide_info) slide_thumbnail() (WSIReader method) SlideGraphConstructor (class in tiatoolbox.tools.graph) SlidingWindowPatchExtractor (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 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.data 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.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.utils module tiatoolbox.utils.env_detection module tiatoolbox.utils.exceptions module tiatoolbox.utils.image module tiatoolbox.utils.metrics module tiatoolbox.utils.misc module tiatoolbox.utils.transforms module tiatoolbox.utils.visualization module tiatoolbox.visualization module tiatoolbox.visualization.tileserver module tiatoolbox.wsicore module tiatoolbox.wsicore.metadata module tiatoolbox.wsicore.metadata.ngff module tiatoolbox.wsicore.save_tiles module tiatoolbox.wsicore.slide_info 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) 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_baseline() (IOSegmentorConfig method) to_dataframe() (AnnotationStore method) (SQLiteStore method) to_feature() (Annotation method) to_geodict() (AnnotationStore method) to_geojson() (Annotation method) (AnnotationStore method) to_ndjson() (AnnotationStore method) to_tile_coords() (AnnotationRenderer static 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) U 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) UpSample2x (class in tiatoolbox.models.architecture.utils) V VahadaneExtractor (class in tiatoolbox.tools.stainextract) VahadaneNormalizer (class in tiatoolbox.tools.stainnorm) validate() (WSIMeta method) 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) VirtualWSIReader (class in tiatoolbox.wsicore.wsireader) visualise() (SlideGraphConstructor class method) W window (Channel attribute) Window (class in tiatoolbox.wsicore.metadata.ngff) 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)