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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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