Convienent handling of annotated whole slide images
Project description
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))
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