Metadata-Version: 2.1
Name: WSI-handling
Version: 0.14.1
Summary: Convienent handling of annotated whole slide images
Home-page: https://github.com/pjl54/WSI_handling/tree/pip_ready
Author: Patrick Leo
Author-email: pjl54@case.edu
License: MIT
Download-URL: https://github.com/pjl54/WSI_handling/archive/v0.13.tar.gz
Keywords: whole slide image,digital pathology,annotations
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.6
Description-Content-Type: text/markdown
Requires-Dist: numpy
Requires-Dist: matplotlib
Requires-Dist: Pillow
Requires-Dist: opencv-python
Requires-Dist: shapely
Requires-Dist: openslide-python

# 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

<?xml version="1.0" encoding="UTF-8"?>
<Annotations>
<Annotation LineColor="65280">
<Regions>
<Region>
<Vertices>
<Vertex X="56657.4765625" Y="78147.3984375"/>
<Vertex X="56657.4765625" Y="78147.3984375"/>
<Vertex X="56664.46875" Y="78147.3984375"/>
</Region>
</Regions>
</Annotation>
</Annotations>

With more <Annotation> or <Region> 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

