API Documentation

• histomicstk
  • utils
    • compute_tile_foreground_fraction()
    • convert_image_to_matrix()
    • convert_matrix_to_image()
    • del2()
    • eigen()
    • exclude_nonfinite()
    • fit_poisson_mixture()
    • gradient_diffusion()
    • hessian()
    • merge_colinear()
    • sample_pixels()
    • simple_mask()
  • preprocessing
    • color space conversion
      • lab_mean_std()
      • lab_to_rgb()
      • od_to_rgb()
      • rgb_to_hsi()
      • rgb_to_lab()
      • rgb_to_od()
      • rgb_to_sda()
      • sda_to_rgb()
    • color deconvolution
      • color_convolution()
      • color_deconvolution()
      • color_deconvolution_routine()
      • complement_stain_matrix()
      • find_stain_index()
      • rgb_separate_stains_macenko_pca()
      • rgb_separate_stains_xu_snmf()
      • separate_stains_macenko_pca()
      • separate_stains_xu_snmf()
      • stain_color_map
      • stain_unmixing_routine()
    • color normalization
      • background_intensity()
      • deconvolution_based_normalization()
      • reinhard()
      • reinhard_stats()
      • reinhard_stats_rgb()
    • data augmentation
      • perturb_stain_concentration()
      • rgb_perturb_stain_concentration()
  • filters
    • edge/gradient filters
      • gaussian_grad()
    • shape filters
      • cdog()
      • clog()
      • glog()
      • vesselness()
  • segmentation
    • embed_boundaries()
    • rag()
    • rag_add_layer()
    • rag_color()
    • simple_mask()
    • label mask processing
      • area_open()
      • compact()
      • condense()
      • delete()
      • delete_border()
      • delete_overlap()
      • dilate_xor()
      • perimeter()
      • remove_overlap_nuclei()
      • shuffle()
      • split()
      • trace_object_boundaries()
      • width_open()
    • level-set segmentation
      • chan_vese()
      • reg_edge()
    • nuclei segmentation
      • detect_nuclei_kofahi()
      • detect_tile_nuclei()
      • gaussian_voting()
      • gvf_tracking()
      • max_clustering()
      • min_model()
    • positive pixel counting
      • Output
        • Output.IntensityAverage
        • Output.IntensityAverageWeakAndPositive
        • Output.IntensitySumPositive
        • Output.IntensitySumStrongPositive
        • Output.IntensitySumWeakPositive
        • Output.NumberPositive
        • Output.NumberStrongPositive
        • Output.NumberTotalPixels
        • Output.NumberWeakPositive
        • Output.RatioStrongToPixels
        • Output.RatioStrongToTotal
        • Output.RatioTotalToPixels
        • Output.RatioWeakToPixels
      • Parameters
        • Parameters.hue_value
        • Parameters.hue_width
        • Parameters.saturation_minimum
        • Parameters.intensity_upper_limit
        • Parameters.intensity_weak_threshold
        • Parameters.intensity_strong_threshold
        • Parameters.intensity_lower_limit
      • count_image()
      • count_slide()
  • features
    • compute_fsd_features()
    • compute_global_cell_graph_features()
    • compute_gradient_features()
    • compute_haralick_features()
    • compute_intensity_features()
    • compute_morphometry_features()
    • compute_nuclei_features()
    • graycomatrixext()
  • annotations and masks
    • Annotation database backup and sqlite parser
      • dump_annotations_locally()
      • dump_annotations_workflow()
      • parse_annotations_to_local_tables()
    • Mosaic review gallery
      • create_review_galleries()
      • get_all_rois_from_folder_v2()
    • Annotations to semantic segmentation masks
      • get_all_rois_from_slide()
      • get_image_and_mask_from_slide()
      • get_mask_from_slide()
      • get_roi_mask()
    • Annotations to object segmentation masks
      • annotations_to_contours_no_mask()
      • combs_with_unique_products()
      • contours_to_labeled_object_mask()
      • get_all_rois_from_slide_v2()
    • Masks to annotations
      • get_annotation_documents_from_contours()
      • get_contours_from_bin_mask()
      • get_contours_from_mask()
      • get_single_annotation_document_from_contours()
    • Annotation and mask utilities
      • create_mask_from_coords()
      • delete_annotations_in_slide()
      • get_bboxes_from_slide_annotations()
      • get_idxs_for_annots_overlapping_roi_by_bbox()
      • get_image_from_htk_response()
      • get_rotated_rectangular_coords()
      • get_scale_factor_and_appendStr()
      • np_vec_no_jit_iou()
      • parse_slide_annotations_into_tables()
      • rotate_point_list()
      • scale_slide_annotations()
    • Polygon merger
      • Polygon_merger
        • Polygon_merger.get_concatenated_contours()
        • Polygon_merger.run()
        • Polygon_merger.set_contours_from_all_masks()
        • Polygon_merger.set_merged_contours()
        • Polygon_merger.set_roi_bboxes()
        • Polygon_merger.set_shared_roi_edges()
      • Polygon_merger_v2
        • Polygon_merger_v2.create_rtree()
        • Polygon_merger_v2.get_merged_multipolygon()
        • Polygon_merger_v2.run()
        • Polygon_merger_v2.run_for_single_group()
        • Polygon_merger_v2.set_contours_slice()
        • Polygon_merger_v2.set_hierarchy()
        • Polygon_merger_v2.set_tree_dict()
  • saliency (tissue/cellularity detection)
    • Tissue detection
      • get_slide_thumbnail()
      • get_tissue_boundary_annotation_documents()
      • get_tissue_mask()
      • threshold_multichannel()
    • Cellularity detection (using thresholding)
      • CDT_single_tissue_piece
        • CDT_single_tissue_piece.assign_components_by_thresholding()
        • CDT_single_tissue_piece.color_normalize_unspecified_components()
        • CDT_single_tissue_piece.find_potentially_cellular_regions()
        • CDT_single_tissue_piece.find_top_cellular_regions()
        • CDT_single_tissue_piece.initialize_labeled_mask()
        • CDT_single_tissue_piece.restrict_mask_to_single_tissue_piece()
        • CDT_single_tissue_piece.run()
        • CDT_single_tissue_piece.set_tissue_rgb()
        • CDT_single_tissue_piece.visualize_results()
      • Cellularity_detector_thresholding
        • Cellularity_detector_thresholding.fix_GTcodes()
        • Cellularity_detector_thresholding.run()
        • Cellularity_detector_thresholding.set_color_normalization_target()
        • Cellularity_detector_thresholding.set_slide_info_and_get_tissue_mask()
    • Cellularity detection (using superpixels)
      • CD_single_tissue_piece
        • CD_single_tissue_piece.assign_cellularity_scores()
        • CD_single_tissue_piece.assign_colors_to_spixel_clusters()
        • CD_single_tissue_piece.restrict_mask_to_single_tissue_piece()
        • CD_single_tissue_piece.run()
        • CD_single_tissue_piece.set_superpixel_assignment()
        • CD_single_tissue_piece.set_superpixel_features()
        • CD_single_tissue_piece.set_superpixel_mask()
        • CD_single_tissue_piece.set_tissue_rgb()
        • CD_single_tissue_piece.visualize_contiguous_superpixels()
        • CD_single_tissue_piece.visualize_individual_superpixels()
      • Cellularity_detector_superpixels
        • Cellularity_detector_superpixels.run()
        • Cellularity_detector_superpixels.set_color_normalization_values()
        • Cellularity_detector_superpixels.set_slide_info_and_get_tissue_mask()
  • workflows
    • Workflow runner
      • Annotation_iterator
        • Annotation_iterator.apply_callback_to_all_annotations()
        • Annotation_iterator.yield_callback_output_for_annotation()
      • Slide_iterator
        • Slide_iterator.run()
        • Slide_iterator.set_slide_ids()
      • Workflow_runner
        • Workflow_runner.run()
    • Specific workflows
      • cellularity_detection_workflow()