Index

_

__add__() (SQLExpression method) __call__() (MultichannelToRGB method) __mul__() (SQLExpression method) _ARRAY_DIMENSIONS (Zattrs attribute)

_creator (Zattrs attribute) _depth (EncoderMixin attribute) _in_channels (EncoderMixin attribute) _out_channels (EncoderMixin attribute) _output_stride (EncoderMixin attribute)

A

activation (Conv2dReLU attribute) (SegmentationHead attribute) 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) argmax_last_axis() (in module tiatoolbox.models.architecture.utils) ArrayView (class in tiatoolbox.wsicore.wsireader) as_dict() (WSIMeta method) assert_dtype_int() (in module tiatoolbox.utils.misc) attention1 (DecoderBlock attribute) attention2 (DecoderBlock attribute) AttentionModule (class in tiatoolbox.models.architecture.utils) augment() (StainAugmentor method) auto_get_mask (MultiTaskSegmentorRunParams attribute) (NucleusDetectorRunParams attribute) (PredictorRunParams attribute) (SemanticSegmentorRunParams attribute) axes (Multiscales attribute) (WSIMeta attribute) Axis (class in tiatoolbox.wsicore.metadata.ngff)

B

background_composite() (in module tiatoolbox.utils.transforms) batch_size (EngineABC attribute) (MultiTaskSegmentorRunParams attribute) (NucleusDetectorRunParams attribute) (PredictorRunParams attribute) (SemanticSegmentorRunParams attribute) bind_cb_obj() (in module tiatoolbox.visualization.bokeh_app.main) bind_cb_obj_tog() (in module tiatoolbox.visualization.bokeh_app.main) blocks (UnetPlusPlusDecoder attribute)

blur_spinner_cb() (in module tiatoolbox.visualization.bokeh_app.main) bounds2locsize() (in module tiatoolbox.utils.transforms) bounds2slices() (in module tiatoolbox.utils.transforms) bounds_at_resolution_to_baseline() (WSIReader method) bquery() (AnnotationStore method) (SQLiteStore method) build() (SlideGraphConstructor static method) build_post_process_raw_predictions() (MultiTaskSegmentor method) build_predicate() (in module tiatoolbox.visualization.bokeh_app.main)

C

canonical_shape() (TIFFWSIReaderDelegate static method) cast_to_min_dtype() (in module tiatoolbox.utils.misc) center (UnetPlusPlusDecoder attribute) CenterBlock (class in tiatoolbox.models.architecture.grandqc) (class in tiatoolbox.models.architecture.kongnet) 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) class_dict (KongNet attribute) (MultiTaskSegmentorRunParams attribute) (NucleusDetectorRunParams attribute) (PredictorRunParams attribute) (SemanticSegmentorRunParams attribute) classifier (CNNModel attribute) (TimmModel attribute) clear() (AnnotationStore method) (SQLiteStore method) cli_auto_get_mask() (in module tiatoolbox.cli.common) cli_batch_size() (in module tiatoolbox.cli.common) cli_class_dict() (in module tiatoolbox.cli.common) cli_device() (in module tiatoolbox.cli.common) cli_file_type() (in module tiatoolbox.cli.common) cli_img_input() (in module tiatoolbox.cli.common) cli_input_resolutions() (in module tiatoolbox.cli.common) cli_masks() (in module tiatoolbox.cli.common) cli_memory_threshold() (in module tiatoolbox.cli.common) cli_method() (in module tiatoolbox.cli.common) cli_min_distance() (in module tiatoolbox.cli.common) cli_mode() (in module tiatoolbox.cli.common) cli_model() (in module tiatoolbox.cli.common) cli_name() (in module tiatoolbox.cli.common) cli_num_workers() (in module tiatoolbox.cli.common) cli_output_file() (in module tiatoolbox.cli.common) cli_output_path() (in module tiatoolbox.cli.common) cli_output_resolutions() (in module tiatoolbox.cli.common) cli_output_type() (in module tiatoolbox.cli.common) cli_overwrite() (in module tiatoolbox.cli.common) cli_patch_input_shape() (in module tiatoolbox.cli.common) cli_patch_mode() (in module tiatoolbox.cli.common) cli_patch_output_shape() (in module tiatoolbox.cli.common) cli_postproc_tile_shape() (in module tiatoolbox.cli.common) cli_region() (in module tiatoolbox.cli.common) cli_resolution() (in module tiatoolbox.cli.common) cli_return_predictions() (in module tiatoolbox.cli.common) cli_return_probabilities() (in module tiatoolbox.cli.common) cli_scale_factor() (in module tiatoolbox.cli.common) cli_stride_shape() (in module tiatoolbox.cli.common) cli_threshold_abs() (in module tiatoolbox.cli.common)

cli_threshold_rel() (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_weights() (in module tiatoolbox.cli.common) cli_yaml_config_path() (in module tiatoolbox.cli.common) clip_probabilities_to_shape() (in module tiatoolbox.models.engine.semantic_segmentor) close() (AnnotationStore method) (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) color (Channel attribute) color_input_cb() (in module tiatoolbox.visualization.bokeh_app.main) ColorbarParamsDict (class in tiatoolbox.utils.visualization) 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) COMMON_GLOBALS_Type (class in tiatoolbox.annotation.dsl) compile_model() (in module tiatoolbox.models.architecture.utils) compile_options() (SQLiteStore static method) compute_annotations() (DaskDelayedJSONStore method) compute_center_of_mass() (in module tiatoolbox.tools.registration.wsi_registration) compute_feature_distances() (DFBRegister static method) compute_qupath_json() (DaskDelayedJSONStore method) con (SQLiteMetadata attribute) concatenate_none() (in module tiatoolbox.models.engine.semantic_segmentor) 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) conv (Conv2dReLU attribute) conv1 (CenterBlock attribute) (DecoderBlock attribute) conv2 (CenterBlock attribute) (DecoderBlock attribute) conv2d (SegmentationHead attribute) Conv2dReLU (class in tiatoolbox.models.architecture.grandqc) ConvBnRelu (class in tiatoolbox.models.architecture.nuclick) convert_metadata() (in module tiatoolbox.utils.tiff_to_fsspec) 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_channel_color_ui() (in module tiatoolbox.visualization.bokeh_app.main) create_index() (SQLiteStore method) create_smart_array() (in module tiatoolbox.utils.misc) 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

DaskDelayedJSONStore (class in tiatoolbox.models.engine.multi_task_segmentor) dataloader (EngineABC attribute), [1] 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) DecoderBlock (class in tiatoolbox.models.architecture.grandqc) (class in tiatoolbox.models.architecture.kongnet) decoders (KongNet attribute) DeepFeatureExtractor (class in tiatoolbox.models.engine.deep_feature_extractor) defaultT (RDefs attribute) defaultZ (RDefs attribute) delaunay_adjacency() (in module tiatoolbox.tools.graph) DenseBlock (class in tiatoolbox.models.architecture.hovernet) depth (UnetPlusPlusDecoder attribute) deserialize_geometry() (AnnotationStore static method) (SQLiteStore method) device (MultiTaskSegmentorRunParams attribute) (NucleusDetectorRunParams attribute) (PredictorRunParams attribute) (SemanticSegmentorRunParams attribute) 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_json_store() (in module tiatoolbox.models.engine.multi_task_segmentor) dict_to_store_patch_predictions() (in module tiatoolbox.utils.misc) dict_to_store_semantic_segmentor() (in module tiatoolbox.utils.misc) DictionaryStore (class in tiatoolbox.annotation.storage) DimensionMismatchError 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) drop_keys (EngineABC attribute) (MultiTaskSegmentor attribute) (NucleusDetector attribute) (NucleusInstanceSegmentor attribute) (PatchPredictor attribute) (SemanticSegmentor attribute) 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) EfficientNetBaseEncoder (class in tiatoolbox.models.architecture.timm_efficientnet) EfficientNetEncoder (class in tiatoolbox.models.architecture.timm_efficientnet) encoder (KongNet attribute) EncoderMixin (class in tiatoolbox.models.architecture.timm_efficientnet) end (Window attribute)

EngineABC (class in tiatoolbox.models.engine.engine_abc) EngineABCRunParams (class in tiatoolbox.models.engine.engine_abc) 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 (CNNBackbone attribute) (CNNModel attribute) (TimmBackbone attribute) (TimmModel 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) 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_bounds_params() (WSIReader 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() (AttentionModule method) (CenterBlock method) (CNNBackbone method) (CNNModel method) (ConvBnRelu method) (DecoderBlock method), [1] (DenseBlock method) (DFBRFeatureExtractor method) (EfficientNetBaseEncoder method) (GrandQCModel method) (HoVerNet method) (KongNet method) (KongNetDecoder method) (MapDe method) (MicroNet method) (ModelABC method) (MultiscaleConvBlock method) (NuClick method) (ResidualBlock method) (ResidualConv method) (SCCNN method) (SCSEModule method) (SubPixelUpsample method) (TFSamepaddingLayer method) (TimmBackbone method) (TimmEncoderFixed method) (TimmModel method) (UnetEncoder method) (UNetModel method) (UnetPlusPlusDecoder method) (UpSample2x method)

forward_hook() (DFBRFeatureExtractor method) from_dataframe() (AnnotationStore class method) from_geojson() (AnnotationStore class method) from_ndjson() (AnnotationStore class method) FsspecJsonWSIReader (class in tiatoolbox.wsicore.wsireader)

G

gather_ui_elements() (in module tiatoolbox.visualization.bokeh_app.main) generate_colors() (MultichannelToRGB method) 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_channel_info() (in module tiatoolbox.visualization.bokeh_app.main) get_channels() (TileServer method) get_color() (AnnotationRenderer method) get_color_prop() (TileServer method) get_concentrations() (StainNormalizer static method) get_connection() (SQLiteStore method) get_coordinates() (PatchExtractor static method) get_dataloader() (EngineABC method) (SemanticSegmentor method) get_efficientnet_kwargs() (in module tiatoolbox.models.architecture.timm_efficientnet) 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_location_array() (TransformedWSIReader method) 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) (TransformedWSIReader method)

get_patch_extractor() (in module tiatoolbox.tools.patchextraction) get_post_proc() (WSIReader method) get_pretrained_model() (in module tiatoolbox.models.architecture) get_properties() (TileServer method) get_property_values() (TileServer method) get_random() (ColorCycler method) get_renderer() (TileServer method) get_secondary_cmap() (TileServer method) get_slide() (TileServer method) get_stages() (EfficientNetBaseEncoder method) (EncoderMixin 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) (TransformedWSIReader method) get_transformed_location_df() (TransformedWSIReader method) get_view_bounds() (in module tiatoolbox.visualization.bokeh_app.main) get_wsi_output_shape() (in module tiatoolbox.models.engine.semantic_segmentor) get_zarr_array() (in module tiatoolbox.utils.misc) glymur_wsi (JP2WSIReader attribute) grab_files_from_dir() (in module tiatoolbox.utils.misc) GrandQCModel (class in tiatoolbox.models.architecture.grandqc) 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) heads (KongNet attribute) healthcheck() (TileServer static method)

hex2rgb() (in module tiatoolbox.visualization.bokeh_app.main) highest_input_resolution (IOInstanceSegmentorConfig attribute) (IOPatchPredictorConfig attribute) (IOSegmentorConfig attribute) (ModelIOConfigABC attribute) 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) images (EngineABC attribute) (MultiTaskSegmentor attribute) (NucleusDetector attribute) (NucleusInstanceSegmentor attribute) (PatchPredictor attribute) (SemanticSegmentor attribute) img (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) (GrandQCModel static method) (HoVerNet static method) (HoVerNetPlus static method) (KongNet static method) (MapDe static method) (MicroNet static method) (ModelABC static method) (NuClick static method) (SCCNN static method) (TimmBackbone static method) (TimmModel static method) (UNetModel static method) infer_patches() (EngineABC method) (MultiTaskSegmentor method) infer_wsi() (DeepFeatureExtractor method) (EngineABC method) (MultiTaskSegmentor method) (SemanticSegmentor 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 (EngineABC attribute), [1] (IOInstanceSegmentorConfig attribute) (IOPatchPredictorConfig attribute) (IOSegmentorConfig attribute) (ModelIOConfigABC attribute) (MultiTaskSegmentor attribute) (NucleusDetector attribute) (NucleusInstanceSegmentor attribute) (PatchPredictor attribute) (SemanticSegmentor attribute) inputs (DatasetInfoABC property) (KatherPatchDataset attribute) (PatchDataset attribute) (WSIPatchDataset attribute) inverted (Channel attribute) ioconfig (EngineABC attribute) (MultiTaskSegmentor attribute) (NucleusDetector attribute) (NucleusInstanceSegmentor attribute) (PatchPredictor attribute) (SemanticSegmentor attribute) IOInstanceSegmentorConfig (class in tiatoolbox.models.engine.io_config) IOPatchPredictorConfig (class in tiatoolbox.models.engine.io_config) IOSegmentorConfig (class in tiatoolbox.models.engine.io_config) 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_torch_compile_compatible() (in module tiatoolbox.models.architecture.utils) is_valid_zarr_fsspec() (FsspecJsonWSIReader static method) 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)

KongNet (class in tiatoolbox.models.architecture.kongnet) KongNetDecoder (class in tiatoolbox.models.architecture.kongnet)

L

lab_split() (ReinhardNormalizer static method) label_names (DatasetInfoABC property) (KatherPatchDataset attribute) labels (DatasetInfoABC property) (EngineABC attribute) (KatherPatchDataset attribute) (MultiTaskSegmentor attribute) (MultiTaskSegmentorRunParams attribute) (NucleusDetectorRunParams attribute) (NucleusInstanceSegmentor attribute) (PatchDataset attribute) (PatchPredictor attribute) (PredictorRunParams attribute) (SemanticSegmentor attribute) (SemanticSegmentorRunParams 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_state_dict() (EfficientNetBaseEncoder method) (KongNet method) load_torch_model() (in module tiatoolbox.models.models_abc) 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) main() (in module tiatoolbox.utils.tiff_to_fsspec) 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_dilated() (EncoderMixin method) 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) margin (IOInstanceSegmentorConfig attribute) (IOSegmentorConfig attribute) masks (EngineABC attribute) (MultiTaskSegmentor attribute) (NucleusDetector attribute) (NucleusInstanceSegmentor attribute) (PatchPredictor attribute) (SemanticSegmentor attribute) match_histograms() (in module tiatoolbox.tools.registration.wsi_registration) max (Window attribute) maxC_target (StainNormalizer attribute) memory_threshold (MultiTaskSegmentorRunParams attribute) (NucleusDetectorRunParams attribute) (PredictorRunParams attribute) (SemanticSegmentorRunParams attribute) merge_back() (ReinhardNormalizer static method) merge_batch_to_canvas() (in module tiatoolbox.models.engine.semantic_segmentor) merge_horizontal() (in module tiatoolbox.models.engine.semantic_segmentor) merge_multitask_horizontal() (in module tiatoolbox.models.engine.multi_task_segmentor) merge_multitask_vertical_chunkwise() (in module tiatoolbox.models.engine.multi_task_segmentor) merge_vertical_chunkwise() (in module tiatoolbox.models.engine.semantic_segmentor) MethodNotSupportedError MicroNet (class in tiatoolbox.models.architecture.micronet) min (Window attribute) min_distance (KongNet attribute) (NucleusDetectorRunParams attribute) min_mask_ratio (PatchExtractor attribute) mode (VirtualWSIReader attribute) model (EngineABC attribute) (MultiTaskSegmentor attribute) (NucleusDetector attribute) (NucleusInstanceSegmentor attribute) (PatchPredictor attribute) (RDefs attribute) (SemanticSegmentor attribute) model_drop_cb() (in module tiatoolbox.visualization.bokeh_app.main) model_to() (in module tiatoolbox.models.models_abc) ModelABC (class in tiatoolbox.models.models_abc) ModelIOConfigABC (class in tiatoolbox.models.engine.io_config) module tiatoolbox tiatoolbox.annotation tiatoolbox.annotation.dsl tiatoolbox.annotation.storage tiatoolbox.cli tiatoolbox.cli.common tiatoolbox.cli.deep_feature_extractor tiatoolbox.cli.multitask_segmentor tiatoolbox.cli.nucleus_detector tiatoolbox.cli.nucleus_instance_segment tiatoolbox.cli.patch_predictor tiatoolbox.cli.read_bounds tiatoolbox.cli.save_tiles tiatoolbox.cli.semantic_segmentor 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.grandqc tiatoolbox.models.architecture.hovernet tiatoolbox.models.architecture.hovernetplus tiatoolbox.models.architecture.idars tiatoolbox.models.architecture.kongnet tiatoolbox.models.architecture.mapde tiatoolbox.models.architecture.micronet tiatoolbox.models.architecture.nuclick tiatoolbox.models.architecture.sccnn tiatoolbox.models.architecture.timm_efficientnet 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.deep_feature_extractor tiatoolbox.models.engine.engine_abc tiatoolbox.models.engine.io_config tiatoolbox.models.engine.multi_task_segmentor tiatoolbox.models.engine.nucleus_detector 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.type_hints tiatoolbox.utils tiatoolbox.utils.env_detection tiatoolbox.utils.exceptions tiatoolbox.utils.image tiatoolbox.utils.magic tiatoolbox.utils.metrics tiatoolbox.utils.misc tiatoolbox.utils.postproc_defs tiatoolbox.utils.tiff_to_fsspec 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) MultichannelToRGB (class in tiatoolbox.utils.postproc_defs) 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) MultiTaskSegmentorRunParams (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) nms_on_detection_maps() (in module tiatoolbox.models.architecture.utils) no_input_message() (in module tiatoolbox.cli.common) node_select_cb() (in module tiatoolbox.visualization.bokeh_app.main) norm (Conv2dReLU attribute) normalize_padding_size() (in module tiatoolbox.utils.image)

nquery() (AnnotationStore method) NucleusDetector (class in tiatoolbox.models.engine.nucleus_detector) NucleusDetectorRunParams (class in tiatoolbox.models.engine.nucleus_detector) NucleusInstanceSegmentor (class in tiatoolbox.models.engine.nucleus_instance_segmentor) NuClick (class in tiatoolbox.models.architecture.nuclick) num_classes (CNNModel attribute) (TimmModel attribute) num_workers (EngineABC attribute) (MultiTaskSegmentorRunParams attribute) (NucleusDetectorRunParams attribute) (PredictorRunParams attribute) (SemanticSegmentorRunParams 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) out_channels (EncoderMixin property) (TimmEncoderFixed property) output_file (MultiTaskSegmentorRunParams attribute) (NucleusDetectorRunParams attribute) (PredictorRunParams attribute) (SemanticSegmentorRunParams attribute) output_locations (MultiTaskSegmentor attribute) (NucleusInstanceSegmentor attribute) (SemanticSegmentor attribute)

output_resolutions (IOInstanceSegmentorConfig attribute) (IOPatchPredictorConfig attribute) (IOSegmentorConfig attribute) (ModelIOConfigABC attribute) (MultiTaskSegmentorRunParams attribute) (NucleusDetectorRunParams attribute) (SemanticSegmentorRunParams attribute) output_stride (EncoderMixin property) (TimmEncoderFixed property) output_tile_size (TilePyramidGenerator property) output_type (EngineABC attribute) (MultiTaskSegmentor attribute) (NucleusDetector attribute) (NucleusInstanceSegmentor attribute) (PatchPredictor attribute) (SemanticSegmentor attribute) 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_bool_list() (in module tiatoolbox.cli.common) parse_cv2_interpolaton() (in module tiatoolbox.utils.misc) parse_generic_tiff_metadata() (TIFFWSIReaderDelegate static method) parse_svs_metadata() (TIFFWSIReaderDelegate static method) patch() (AnnotationStore method) (DictionaryStore method) patch_first_conv() (in module tiatoolbox.models.architecture.timm_efficientnet) patch_input_shape (EngineABC attribute), [1] (IOInstanceSegmentorConfig attribute) (IOPatchPredictorConfig attribute) (IOSegmentorConfig attribute) (ModelIOConfigABC attribute) (MultiTaskSegmentor attribute) (NucleusDetector attribute) (NucleusInstanceSegmentor attribute) (PatchDataset attribute) (PatchPredictor attribute) (SemanticSegmentor attribute) (WSIPatchDataset attribute) patch_many() (AnnotationStore method) (SQLiteStore method) patch_mode (EngineABC attribute) (MultiTaskSegmentor attribute) (NucleusDetector attribute) (NucleusInstanceSegmentor attribute) (PatchPredictor attribute) (SemanticSegmentor attribute) patch_output_shape (IOInstanceSegmentorConfig attribute) (IOSegmentorConfig attribute) (MultiTaskSegmentorRunParams attribute) (NucleusDetectorRunParams attribute) (SemanticSegmentorRunParams attribute) patch_predictions_as_annotations() (in module tiatoolbox.utils.misc) patch_predictions_as_qupath_json() (in module tiatoolbox.utils.misc) patch_size (PatchExtractor attribute) PatchDataset (class in tiatoolbox.models.dataset.dataset_abc) 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) peak_detection_map_overlap() (in module tiatoolbox.models.architecture.utils) 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 (CNNBackbone attribute) (CNNModel attribute)

populate_layer_list() (in module tiatoolbox.visualization.bokeh_app.main) populate_slide_list() (in module tiatoolbox.visualization.bokeh_app.main) populate_table() (in module tiatoolbox.visualization.bokeh_app.main) post_process_patches() (DeepFeatureExtractor method) (EngineABC method) (MultiTaskSegmentor method) (NucleusDetector method) (PatchPredictor method) post_process_wsi() (EngineABC method) (MultiTaskSegmentor method) (NucleusDetector method) (PatchPredictor method) postproc() (CNNModel static method) (GrandQCModel static method) (HoVerNet method) (HoVerNetPlus method) (KongNet method) (MapDe method) (MicroNet method) (ModelABC static method) (NuClick static method) (SCCNN method) (TimmModel static method) (UNetModel 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) PredictorRunParams (class in tiatoolbox.models.engine.patch_predictor) prepare_engines_save_dir() (in module tiatoolbox.models.engine.engine_abc) prepare_file_dir_cli() (in module tiatoolbox.cli.common) prepare_full_batch() (in module tiatoolbox.models.engine.semantic_segmentor) prepare_ioconfig() (in module tiatoolbox.cli.common) prepare_model_cli() (in module tiatoolbox.cli.common) prepare_multitask_full_batch() (in module tiatoolbox.models.engine.multi_task_segmentor) preproc() (GrandQCModel static method) (IDaRS static method) (KongNet static method) (MicroNet static method) (ModelABC static method) (PatchDatasetABC static method) (SCCNN static method) preproc_func (ModelABC property) (PatchDatasetABC property) (WSIPatchDataset attribute) pretrained (TimmModel attribute) process_contours() (in module tiatoolbox.utils.misc) process_prediction_per_batch (DeepFeatureExtractor 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) (FsspecJsonWSIReader method) (JP2WSIReader method) (NGFFWSIReader method) (OpenSlideWSIReader method) (TIFFWSIReader method) (TIFFWSIReaderDelegate method) (TransformedWSIReader method) (VirtualWSIReader method) (WSIReader method) read_locations() (in module tiatoolbox.utils.misc) read_rect() (AffineWSITransformer method) (AnnotationStoreReader method) (DICOMWSIReader method) (FsspecJsonWSIReader method) (JP2WSIReader method) (NGFFWSIReader method) (OpenSlideWSIReader method) (TIFFWSIReader method) (TIFFWSIReaderDelegate method) (TransformedWSIReader method) (VirtualWSIReader method) (WSIReader method) read_rect_at_resolution() (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)

render_pts() (AnnotationRenderer method) replace_strides_with_dilation() (in module tiatoolbox.models.architecture.timm_efficientnet) replace_url() (in module tiatoolbox.utils.tiff_to_fsspec) 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) retrieve_sel_uids() (in module tiatoolbox.models.engine.multi_task_segmentor) return_labels (EngineABC attribute), [1] (MultiTaskSegmentor attribute) (MultiTaskSegmentorRunParams attribute) (NucleusDetector attribute) (NucleusDetectorRunParams attribute) (NucleusInstanceSegmentor attribute) (PatchPredictor attribute) (PredictorRunParams attribute) (SemanticSegmentor attribute) (SemanticSegmentorRunParams attribute) return_predictions (MultiTaskSegmentorRunParams attribute) return_predictions_dict (MultiTaskSegmentor attribute) (NucleusInstanceSegmentor attribute) return_probabilities (MultiTaskSegmentorRunParams attribute) (NucleusDetectorRunParams attribute) (PredictorRunParams attribute) (SemanticSegmentorRunParams 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) run() (DeepFeatureExtractor method) (EngineABC method) (MultiTaskSegmentor method) (NucleusDetector method) (PatchPredictor method) (SemanticSegmentor method) 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) sample_image_opencv() (TransformedWSIReader static method) save_annotations() (in module tiatoolbox.utils.misc) save_as_json() (in module tiatoolbox.utils.misc) save_cb() (in module tiatoolbox.visualization.bokeh_app.main) save_detection_arrays_to_qupath_json() (in module tiatoolbox.models.engine.nucleus_detector) save_detection_arrays_to_store() (in module tiatoolbox.models.engine.nucleus_detector) save_multitask_to_cache() (in module tiatoolbox.models.engine.multi_task_segmentor) save_predictions() (DeepFeatureExtractor method) (EngineABC method) (MultiTaskSegmentor method) (NucleusDetector method) (SemanticSegmentor method) save_predictions_as_zarr() (EngineABC method) save_qupath_json() (in module tiatoolbox.utils.misc) save_resolution (IOInstanceSegmentorConfig attribute) (IOSegmentorConfig attribute) save_tiles() (WSIReader method) save_to_cache() (in module tiatoolbox.models.engine.deep_feature_extractor) (in module tiatoolbox.models.engine.semantic_segmentor) save_yaml() (in module tiatoolbox.utils.misc) scale (CoordinateTransform attribute) scale_factor (MultiTaskSegmentorRunParams attribute) (NucleusDetectorRunParams attribute) (PredictorRunParams attribute) (SemanticSegmentorRunParams attribute) scale_spinner_cb() (in module tiatoolbox.visualization.bokeh_app.main) scale_to_highest() (ModelIOConfigABC static method) SCCNN (class in tiatoolbox.models.architecture.sccnn) SCSEModule (class in tiatoolbox.models.architecture.utils) search() (SQLRegex class method) segment_on_box() (in module tiatoolbox.visualization.bokeh_app.main) SegmentationHead (class in tiatoolbox.models.architecture.utils) select_cv2_interpolation() (in module tiatoolbox.utils.misc) select_device() (in module tiatoolbox.utils.misc) SemanticSegmentor (class in tiatoolbox.models.engine.semantic_segmentor) SemanticSegmentorRunParams (class in tiatoolbox.models.engine.semantic_segmentor) serialise_geometry() (AnnotationStore static method) (SQLiteStore method) session_id() (TileServer method) sessions() (TileServer method) set_alpha_glyph() (in module tiatoolbox.visualization.bokeh_app.main) set_channel_info() (in module tiatoolbox.visualization.bokeh_app.main) set_channels() (TileServer method) set_enhance() (TileServer method) set_in_channels() (EncoderMixin method) 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) store_probabilities() (in module tiatoolbox.models.engine.semantic_segmentor) stride (PatchExtractor attribute) (SlidingWindowPatchExtractor attribute) stride_shape (EngineABC attribute), [1] (IOInstanceSegmentorConfig attribute) (IOPatchPredictorConfig attribute) (IOSegmentorConfig attribute) (ModelIOConfigABC attribute) (MultiTaskSegmentor attribute) (MultiTaskSegmentorRunParams attribute) (NucleusDetector attribute) (NucleusDetectorRunParams attribute) (NucleusInstanceSegmentor attribute) (PatchPredictor attribute) (PredictorRunParams attribute) (SemanticSegmentor attribute) (SemanticSegmentorRunParams attribute) string_to_tuple() (in module tiatoolbox.utils.misc) sub_pixel_read() (in module tiatoolbox.utils.image) sub_tile_level_count (TilePyramidGenerator property) SubPixelUpsample (class in tiatoolbox.models.architecture.kongnet)

T

tap_event_cb() (in module tiatoolbox.visualization.bokeh_app.main) tap_query() (TileServer method) target_channels (KongNet attribute) target_concentrations (StainNormalizer attribute) target_means (ReinhardNormalizer attribute) target_stds (ReinhardNormalizer attribute) TFSamepaddingLayer (class in tiatoolbox.models.architecture.hovernet) threshold_abs (KongNet attribute) (NucleusDetectorRunParams attribute) threshold_rel (NucleusDetectorRunParams attribute) tiatoolbox module tiatoolbox.annotation module tiatoolbox.annotation.dsl module tiatoolbox.annotation.storage module tiatoolbox.cli module tiatoolbox.cli.common module tiatoolbox.cli.deep_feature_extractor module tiatoolbox.cli.multitask_segmentor module tiatoolbox.cli.nucleus_detector 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_segmentor 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.grandqc module tiatoolbox.models.architecture.hovernet module tiatoolbox.models.architecture.hovernetplus module tiatoolbox.models.architecture.idars module tiatoolbox.models.architecture.kongnet module tiatoolbox.models.architecture.mapde module tiatoolbox.models.architecture.micronet module tiatoolbox.models.architecture.nuclick module tiatoolbox.models.architecture.sccnn module tiatoolbox.models.architecture.timm_efficientnet 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.deep_feature_extractor module tiatoolbox.models.engine.engine_abc module tiatoolbox.models.engine.io_config module tiatoolbox.models.engine.multi_task_segmentor module tiatoolbox.models.engine.nucleus_detector 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.type_hints 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.postproc_defs module tiatoolbox.utils.tiff_to_fsspec 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) TIFFWSIReaderDelegate (class in tiatoolbox.wsicore.wsireader) tile_grid_size() (TilePyramidGenerator method) tile_group() (ZoomifyGenerator method) tile_path() (TilePyramidGenerator method) (ZoomifyGenerator method) tile_shape (IOInstanceSegmentorConfig attribute) (IOSegmentorConfig attribute) (KongNet attribute) (NucleusDetectorRunParams attribute) TileGroup (class in tiatoolbox.visualization.bokeh_app.main) TilePyramidGenerator (class in tiatoolbox.tools.pyramid) TileServer (class in tiatoolbox.visualization.tileserver) TimmBackbone (class in tiatoolbox.models.architecture.vanilla) TimmEncoderFixed (class in tiatoolbox.models.architecture.kongnet) TimmModel (class in tiatoolbox.models.architecture.vanilla) tissue_mask (StainAugmentor attribute) tissue_mask() (WSIReader method) TissueMasker (class in tiatoolbox.tools.tissuemask) to() (ModelABC method) to_baseline() (IOInstanceSegmentorConfig method) (IOSegmentorConfig method) (ModelIOConfigABC 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) tqdm_dask_progress_bar() (in module tiatoolbox.utils.misc) transform() (AnnotationStore method) (MorphologicalMasker method) (OtsuTissueMasker method) (ReinhardNormalizer method) (StainNormalizer method) (TissueMasker method) transform_patch() (AffineWSITransformer method) (TransformedWSIReader method) transform_points() (AffineWSITransformer static method) (TransformedWSIReader static method) transform_using_disp_array() (TransformedWSIReader static method) TransformedWSIReader (class in tiatoolbox.wsicore.wsireader) triangle_signed_area() (in module tiatoolbox.tools.graph) try_annotation_store() (WSIReader static method) try_dicom() (WSIReader static method) try_fsspec() (WSIReader static method) try_ngff() (WSIReader static method) try_ome_tiff() (WSIReader static method) try_tiff() (WSIReader static method) 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) UnetPlusPlusDecoder (class in tiatoolbox.models.architecture.grandqc) 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_tqdm_desc() (in module tiatoolbox.utils.misc) update_types() (TileServer static method) update_ui_on_new_annotations() (in module tiatoolbox.visualization.bokeh_app.main) UpSample2x (class in tiatoolbox.models.architecture.utils) upsampling_layer (SegmentationHead attribute)

V

VahadaneExtractor (class in tiatoolbox.tools.stainextract) VahadaneNormalizer (class in tiatoolbox.tools.stainnorm) validate() (MultichannelToRGB method) (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 (EngineABC attribute), [1] (MultiTaskSegmentorRunParams attribute) (NucleusDetectorRunParams attribute) (PredictorRunParams attribute) (SemanticSegmentorRunParams 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)

write_probability_heatmap_as_ome_tiff() (in module tiatoolbox.utils.misc) wsi (PatchExtractor attribute) WSIMeta (class in tiatoolbox.wsicore.wsimeta) WSIPatchDataset (class in tiatoolbox.models.dataset.dataset_abc) WSIReader (class in tiatoolbox.wsicore.wsireader)

Z

Zattrs (class in tiatoolbox.wsicore.metadata.ngff)

zoomify() (TileServer method) ZoomifyGenerator (class in tiatoolbox.tools.pyramid)