WSI-handling 0.13

Convienent handling of annotated whole slide images

WSI_handling

Code snippets for handling digital pathology pyramidal whole slide images (WSIs). Currently only works with annotation XMLs from Aperio ImageScope and image formats supported by Openslide.

Supports getting a tile from a WSI at the desired micron-per-pixel (mpp), getting either the whole WSI or an annotated region, generating a mask image for either a tile or the WSIs, and showing the location of a tile on the WSI.

Annotation format

Annotations must follow the AperioImagescope format

With more or blocks for additional annotations.

Usage

from WSI_handling import wsi

xml_fname=r'/mnt/data/home/pjl54/UPenn_prostate/20698.xml' img_fname=r'/mnt/data/home/pjl54/UPenn_prostate/20698.svs' w = wsi(img_fname,xml_fname)

wsi_img = w.get_wsi(desired_mpp=4)); ROI, mask = w.get_annotated_region(desired_mpp=2,colors_to_use='green',annotation_idx='largest',mask_out_roi=False) tile = w.get_tile(desired_mpp=1,coords=(10000,25000),wh=(2000,2000)) tile_mask = w.mask_out_tile(desired_mpp=1,coords=(10000,25000),wh=(2000,2000))) tile_location = w.show_tile_location(desired_mpp=1,coords=(10000,25000),wh=(2000,2000))