Generates a coloring of an adjacency graph using the sequential coloring algorithm. Used to bin regions from a label image into a small number of

Distance-regularized edge-based level sets. Distance-regularization is used in this edge-based level set implementation to avoid numerical pr

Samples a whole-slide-image to determine colorspace statistics (mean, variance) needed to perform global Reinhard color normalization. Normal

Remove overlapping nuclei using spatial indexing and parallel processing. This function removes overlapping nuclei polygons from input using

Reproduce annotations on HistomicsUI from local backup. This is the reverse functionality to dump_annotations.locally(). This reproduces this

Revert an annotation to a previous version. Parameters ---------- gc : girder_client.GirderClient authenticated girder client

Revert all annotations in a folder recursively. Parameters ---------- gc : girder_client.GirderClient authenticated girder client

Compute the stain matrix for color deconvolution with SNMF from an RGB image or matrix. Parameters ---------- im_rgb : array_like

Generates a sampling of pixels from a whole-slide image. Useful for generating statistics or Reinhard color-normalization or adaptive deconvo

Set color normalization values to use from target image. Arguments: --------- ref_image_path, str > path to target

Shuffles labels in a label image to improve visualization and enhance object boundaries. Parameters ---------- im_label : array_

Re-labels objects that have multiple non-contiguous portions to create a new label image where each object is contiguous. Parameters ----

Split a Namespace into a Namespace of Namespaces based on shared prefixes. The string separating the prefix from the rest of the argument is

Test Slide_iterator.run().

Test annotations_to_contours_no_mask().

Test get_image_and_mask_from_slide().

Test Cellularity_detector_superpixels().

Test Cellularity_detector_thresholding().

Test create_review_galleries().

Test dump annotations locally.

Test dump annotations locally.

Test get_all_rois_from_folder_v2().

Test get_all_roi_masks_for_slide() as-is without tiling.

Test get_all_roi_masks_for_slide() with tiling.

Test get_all_rois_from_slide_v2().

Test get_contours_from_bin_mask().

Test get_bboxes_from_slide_annotations.

Test get_contours_from_mask().

Test get_contours_from_mask().

Test get_contours_from_mask().

Test get_image_and_mask_from_slide().

Test get_image_and_mask_from_slide().

Test get_image_from_htk_response.

Test get_roi_mask().

Test get_scale_factor_and_appendStr.

Test get_tissue_boundary_annotation_documents().

Test get_tissue_mask().

Test macenko_pca normalization.

Test parse_slide_annotations_into_tables.

Test Polygon_merger_v2.run().

Test Polygon_merger.run().

Test reinhard.

Test rgb_perturb_stain_concentration.

Test workflow runner for cellularity detection.

Test scale_slide_annotations.

Placeholder.

Update permissions for a single annotation. Parameters ---------- gc : gider_client.GirderClient authenticated girder client inst