# 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.

# Usage
See wsi_demo.ipynb

# TODO

~~Add support for .scn images (OpenSlide reads .scn images in rotated by 270 degrees relative to how ImageScope reads them)~~

~~Add fuction to get tile of annotated region~~

Add support for Bioformats

