PenAnnotationExtractor

Pen annotation extraction from WSI.

This is the code for the paper:

Schüffler PJ, Yarlagadda DVK, Vanderbilt C, Fuchs TJ: Overcoming an Annotation Hurdle: Digitizing Pen Annotations from Whole Slide Images. Journal of Pathology Informatics, 2021

Uses Python 3.7+

Install requirements:

pip install -r requirements.txt

Run the code

1. To create the extractions, run

   python penAnnotationExtractor.py

2. Optionally to compare to manual annotations, run

   python validation.py