Index

A

Annotation_iterator (class in histomicstk.workflows.workflow_runner) annotations_to_contours_no_mask() (in module histomicstk.annotations_and_masks.annotations_to_object_mask_handler) apply_callback_to_all_annotations() (histomicstk.workflows.workflow_runner.Annotation_iterator method)

area_open() (in module histomicstk.segmentation.label) assign_cellularity_scores() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method) assign_colors_to_spixel_clusters() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method) assign_components_by_thresholding() (histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method)

B

background_intensity() (in module histomicstk.preprocessing.color_normalization)

C

CD_single_tissue_piece (class in histomicstk.saliency.cellularity_detection_superpixels) cdog() (in module histomicstk.filters.shape) CDT_single_tissue_piece (class in histomicstk.saliency.cellularity_detection_thresholding) cellularity_detection_workflow() (in module histomicstk.workflows.specific_workflows) Cellularity_detector_superpixels (class in histomicstk.saliency.cellularity_detection_superpixels) Cellularity_detector_thresholding (class in histomicstk.saliency.cellularity_detection_thresholding) chan_vese() (in module histomicstk.segmentation.level_set) clog() (in module histomicstk.filters.shape) color_convolution() (in module histomicstk.preprocessing.color_deconvolution) color_deconvolution() (in module histomicstk.preprocessing.color_deconvolution) color_deconvolution_routine() (in module histomicstk.preprocessing.color_deconvolution) color_normalize_unspecified_components() (histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method) combs_with_unique_products() (in module histomicstk.annotations_and_masks.annotations_to_object_mask_handler) compact() (in module histomicstk.segmentation.label) complement_stain_matrix() (in module histomicstk.preprocessing.color_deconvolution) compute_fsd_features() (in module histomicstk.features)

compute_global_cell_graph_features() (in module histomicstk.features) compute_gradient_features() (in module histomicstk.features) compute_haralick_features() (in module histomicstk.features) compute_intensity_features() (in module histomicstk.features) compute_morphometry_features() (in module histomicstk.features) compute_nuclei_features() (in module histomicstk.features) compute_tile_foreground_fraction() (in module histomicstk.utils) condense() (in module histomicstk.segmentation.label) contours_to_labeled_object_mask() (in module histomicstk.annotations_and_masks.annotations_to_object_mask_handler) convert_image_to_matrix() (in module histomicstk.utils) convert_matrix_to_image() (in module histomicstk.utils) count_image() (in module histomicstk.segmentation.positive_pixel_count) count_slide() (in module histomicstk.segmentation.positive_pixel_count) create_mask_from_coords() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils) create_review_galleries() (in module histomicstk.annotations_and_masks.review_gallery) create_rtree() (histomicstk.annotations_and_masks.polygon_merger_v2.Polygon_merger_v2 method)

D

deconvolution_based_normalization() (in module histomicstk.preprocessing.color_normalization) del2() (in module histomicstk.utils) delete() (in module histomicstk.segmentation.label) delete_annotations_in_slide() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils) delete_border() (in module histomicstk.segmentation.label)

delete_overlap() (in module histomicstk.segmentation.label) detect_nuclei_kofahi() (in module histomicstk.segmentation.nuclear) detect_tile_nuclei() (in module histomicstk.segmentation.nuclear) dilate_xor() (in module histomicstk.segmentation.label) dump_annotations_locally() (in module histomicstk.annotations_and_masks.annotation_database_parser) dump_annotations_workflow() (in module histomicstk.annotations_and_masks.annotation_database_parser)

E

eigen() (in module histomicstk.utils)

embed_boundaries() (in module histomicstk.segmentation) exclude_nonfinite() (in module histomicstk.utils)

F

find_potentially_cellular_regions() (histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method) find_stain_index() (in module histomicstk.preprocessing.color_deconvolution)

find_top_cellular_regions() (histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method) fit_poisson_mixture() (in module histomicstk.utils) fix_GTcodes() (histomicstk.saliency.cellularity_detection_thresholding.Cellularity_detector_thresholding method)

G

gaussian_grad() (in module histomicstk.filters.edge) gaussian_voting() (in module histomicstk.segmentation.nuclear) get_all_rois_from_folder_v2() (in module histomicstk.annotations_and_masks.review_gallery) get_all_rois_from_slide() (in module histomicstk.annotations_and_masks.annotations_to_masks_handler) get_all_rois_from_slide_v2() (in module histomicstk.annotations_and_masks.annotations_to_object_mask_handler) get_annotation_documents_from_contours() (in module histomicstk.annotations_and_masks.masks_to_annotations_handler) get_bboxes_from_slide_annotations() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils) get_concatenated_contours() (histomicstk.annotations_and_masks.polygon_merger.Polygon_merger method) get_contours_from_bin_mask() (in module histomicstk.annotations_and_masks.masks_to_annotations_handler) get_contours_from_mask() (in module histomicstk.annotations_and_masks.masks_to_annotations_handler) get_idxs_for_annots_overlapping_roi_by_bbox() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils) get_image_and_mask_from_slide() (in module histomicstk.annotations_and_masks.annotations_to_masks_handler) get_image_from_htk_response() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils)

get_mask_from_slide() (in module histomicstk.annotations_and_masks.annotations_to_masks_handler) get_merged_multipolygon() (histomicstk.annotations_and_masks.polygon_merger_v2.Polygon_merger_v2 method) get_roi_mask() (in module histomicstk.annotations_and_masks.annotations_to_masks_handler) get_rotated_rectangular_coords() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils) get_scale_factor_and_appendStr() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils) get_single_annotation_document_from_contours() (in module histomicstk.annotations_and_masks.masks_to_annotations_handler) get_slide_thumbnail() (in module histomicstk.saliency.tissue_detection) get_tissue_boundary_annotation_documents() (in module histomicstk.saliency.tissue_detection) get_tissue_mask() (in module histomicstk.saliency.tissue_detection) glog() (in module histomicstk.filters.shape) gradient_diffusion() (in module histomicstk.utils) graycomatrixext() (in module histomicstk.features) gvf_tracking() (in module histomicstk.segmentation.nuclear)

H

hessian() (in module histomicstk.utils) histomicstk.annotations_and_masks module histomicstk.annotations_and_masks.annotation_and_mask_utils module histomicstk.annotations_and_masks.annotation_database_parser module histomicstk.annotations_and_masks.annotations_to_masks_handler module histomicstk.annotations_and_masks.annotations_to_object_mask_handler module histomicstk.annotations_and_masks.masks_to_annotations_handler module histomicstk.annotations_and_masks.polygon_merger module histomicstk.annotations_and_masks.polygon_merger_v2 module histomicstk.annotations_and_masks.review_gallery module histomicstk.features module histomicstk.filters module histomicstk.filters.edge module histomicstk.filters.shape module histomicstk.preprocessing module histomicstk.preprocessing.augmentation module histomicstk.preprocessing.color_conversion module

histomicstk.preprocessing.color_deconvolution module histomicstk.preprocessing.color_normalization module histomicstk.saliency module histomicstk.saliency.cellularity_detection_superpixels module histomicstk.saliency.cellularity_detection_thresholding module histomicstk.saliency.tissue_detection module histomicstk.segmentation module histomicstk.segmentation.label module histomicstk.segmentation.level_set module histomicstk.segmentation.nuclear module histomicstk.segmentation.positive_pixel_count module histomicstk.utils module histomicstk.workflows module histomicstk.workflows.specific_workflows module histomicstk.workflows.workflow_runner module hue_value (histomicstk.segmentation.positive_pixel_count.Parameters attribute) hue_width (histomicstk.segmentation.positive_pixel_count.Parameters attribute)

I

initialize_labeled_mask() (histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method) intensity_lower_limit (histomicstk.segmentation.positive_pixel_count.Parameters attribute) intensity_strong_threshold (histomicstk.segmentation.positive_pixel_count.Parameters attribute) intensity_upper_limit (histomicstk.segmentation.positive_pixel_count.Parameters attribute) intensity_weak_threshold (histomicstk.segmentation.positive_pixel_count.Parameters attribute)

IntensityAverage (histomicstk.segmentation.positive_pixel_count.Output attribute) IntensityAverageWeakAndPositive (histomicstk.segmentation.positive_pixel_count.Output attribute) IntensitySumPositive (histomicstk.segmentation.positive_pixel_count.Output attribute) IntensitySumStrongPositive (histomicstk.segmentation.positive_pixel_count.Output attribute) IntensitySumWeakPositive (histomicstk.segmentation.positive_pixel_count.Output attribute)

L

lab_mean_std() (in module histomicstk.preprocessing.color_conversion)

lab_to_rgb() (in module histomicstk.preprocessing.color_conversion)

M

max_clustering() (in module histomicstk.segmentation.nuclear) merge_colinear() (in module histomicstk.utils) min_model() (in module histomicstk.segmentation.nuclear) module histomicstk.annotations_and_masks histomicstk.annotations_and_masks.annotation_and_mask_utils histomicstk.annotations_and_masks.annotation_database_parser histomicstk.annotations_and_masks.annotations_to_masks_handler histomicstk.annotations_and_masks.annotations_to_object_mask_handler histomicstk.annotations_and_masks.masks_to_annotations_handler histomicstk.annotations_and_masks.polygon_merger histomicstk.annotations_and_masks.polygon_merger_v2 histomicstk.annotations_and_masks.review_gallery histomicstk.features histomicstk.filters histomicstk.filters.edge histomicstk.filters.shape histomicstk.preprocessing histomicstk.preprocessing.augmentation histomicstk.preprocessing.color_conversion histomicstk.preprocessing.color_deconvolution histomicstk.preprocessing.color_normalization histomicstk.saliency histomicstk.saliency.cellularity_detection_superpixels histomicstk.saliency.cellularity_detection_thresholding histomicstk.saliency.tissue_detection histomicstk.segmentation histomicstk.segmentation.label histomicstk.segmentation.level_set histomicstk.segmentation.nuclear histomicstk.segmentation.positive_pixel_count histomicstk.utils histomicstk.workflows histomicstk.workflows.specific_workflows histomicstk.workflows.workflow_runner

N

np_vec_no_jit_iou() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils) NumberPositive (histomicstk.segmentation.positive_pixel_count.Output attribute)

NumberStrongPositive (histomicstk.segmentation.positive_pixel_count.Output attribute) NumberTotalPixels (histomicstk.segmentation.positive_pixel_count.Output attribute) NumberWeakPositive (histomicstk.segmentation.positive_pixel_count.Output attribute)

O

od_to_rgb() (in module histomicstk.preprocessing.color_conversion)

Output (class in histomicstk.segmentation.positive_pixel_count)

P

Parameters (class in histomicstk.segmentation.positive_pixel_count) parse_annotations_to_local_tables() (in module histomicstk.annotations_and_masks.annotation_database_parser) parse_slide_annotations_into_tables() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils)

perimeter() (in module histomicstk.segmentation.label) perturb_stain_concentration() (in module histomicstk.preprocessing.augmentation) Polygon_merger (class in histomicstk.annotations_and_masks.polygon_merger) Polygon_merger_v2 (class in histomicstk.annotations_and_masks.polygon_merger_v2)

R

rag() (in module histomicstk.segmentation) rag_add_layer() (in module histomicstk.segmentation) rag_color() (in module histomicstk.segmentation) RatioStrongToPixels (histomicstk.segmentation.positive_pixel_count.Output attribute) RatioStrongToTotal (histomicstk.segmentation.positive_pixel_count.Output attribute) RatioTotalToPixels (histomicstk.segmentation.positive_pixel_count.Output attribute) RatioWeakToPixels (histomicstk.segmentation.positive_pixel_count.Output attribute) reg_edge() (in module histomicstk.segmentation.level_set) reinhard() (in module histomicstk.preprocessing.color_normalization) reinhard_stats() (in module histomicstk.preprocessing.color_normalization) reinhard_stats_rgb() (in module histomicstk.preprocessing.color_normalization) remove_overlap_nuclei() (in module histomicstk.segmentation.label) restrict_mask_to_single_tissue_piece() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method) (histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method) rgb_perturb_stain_concentration() (in module histomicstk.preprocessing.augmentation)

rgb_separate_stains_macenko_pca() (in module histomicstk.preprocessing.color_deconvolution) rgb_separate_stains_xu_snmf() (in module histomicstk.preprocessing.color_deconvolution) rgb_to_hsi() (in module histomicstk.preprocessing.color_conversion) rgb_to_lab() (in module histomicstk.preprocessing.color_conversion) rgb_to_od() (in module histomicstk.preprocessing.color_conversion) rgb_to_sda() (in module histomicstk.preprocessing.color_conversion) rotate_point_list() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils) run() (histomicstk.annotations_and_masks.polygon_merger.Polygon_merger method) (histomicstk.annotations_and_masks.polygon_merger_v2.Polygon_merger_v2 method) (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method) (histomicstk.saliency.cellularity_detection_superpixels.Cellularity_detector_superpixels method) (histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method) (histomicstk.saliency.cellularity_detection_thresholding.Cellularity_detector_thresholding method) (histomicstk.workflows.workflow_runner.Slide_iterator method) (histomicstk.workflows.workflow_runner.Workflow_runner method) run_for_single_group() (histomicstk.annotations_and_masks.polygon_merger_v2.Polygon_merger_v2 method)

S

sample_pixels() (in module histomicstk.utils) saturation_minimum (histomicstk.segmentation.positive_pixel_count.Parameters attribute) scale_slide_annotations() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils) sda_to_rgb() (in module histomicstk.preprocessing.color_conversion) separate_stains_macenko_pca() (in module histomicstk.preprocessing.color_deconvolution) separate_stains_xu_snmf() (in module histomicstk.preprocessing.color_deconvolution) set_color_normalization_target() (histomicstk.saliency.cellularity_detection_thresholding.Cellularity_detector_thresholding method) set_color_normalization_values() (histomicstk.saliency.cellularity_detection_superpixels.Cellularity_detector_superpixels method) set_contours_from_all_masks() (histomicstk.annotations_and_masks.polygon_merger.Polygon_merger method) set_contours_slice() (histomicstk.annotations_and_masks.polygon_merger_v2.Polygon_merger_v2 method) set_hierarchy() (histomicstk.annotations_and_masks.polygon_merger_v2.Polygon_merger_v2 method) set_merged_contours() (histomicstk.annotations_and_masks.polygon_merger.Polygon_merger method) set_roi_bboxes() (histomicstk.annotations_and_masks.polygon_merger.Polygon_merger method) set_shared_roi_edges() (histomicstk.annotations_and_masks.polygon_merger.Polygon_merger method) set_slide_ids() (histomicstk.workflows.workflow_runner.Slide_iterator method)

set_slide_info_and_get_tissue_mask() (histomicstk.saliency.cellularity_detection_superpixels.Cellularity_detector_superpixels method) (histomicstk.saliency.cellularity_detection_thresholding.Cellularity_detector_thresholding method) set_superpixel_assignment() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method) set_superpixel_features() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method) set_superpixel_mask() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method) set_tissue_rgb() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method) (histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method) set_tree_dict() (histomicstk.annotations_and_masks.polygon_merger_v2.Polygon_merger_v2 method) shuffle() (in module histomicstk.segmentation.label) simple_mask() (in module histomicstk.segmentation) (in module histomicstk.utils) Slide_iterator (class in histomicstk.workflows.workflow_runner) split() (in module histomicstk.segmentation.label) stain_color_map (in module histomicstk.preprocessing.color_deconvolution) stain_unmixing_routine() (in module histomicstk.preprocessing.color_deconvolution)

T

threshold_multichannel() (in module histomicstk.saliency.tissue_detection)

trace_object_boundaries() (in module histomicstk.segmentation.label)

V

vesselness() (in module histomicstk.filters.shape) visualize_contiguous_superpixels() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method)

visualize_individual_superpixels() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method) visualize_results() (histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method)

W

width_open() (in module histomicstk.segmentation.label)

Workflow_runner (class in histomicstk.workflows.workflow_runner)

Y

yield_callback_output_for_annotation() (histomicstk.workflows.workflow_runner.Annotation_iterator method)