Convienent handling of annotated whole slide images
Project description
WSI_handling
Code for handling digital pathology pyramidal whole slide images (WSIs). Currently works with annotation XMLs from Aperio ImageScope or annotation json's from QuPath 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
XML annotations must follow the AperioImagescope format
With more or blocks for additional annotations.
json annotations must follow QuPath's json export format.
Installation
pip install WSI_handling
Usage
See https://github.com/pjl54/WSI_handling/blob/master/wsi_demo.ipynb
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