This repository contains a collection of Groovy scripts designed to enhance and automate various tasks within QuPath, a powerful open-source software for bioimage analysis, particularly in digital pathology. These scripts are intended to help pathologists and researchers efficiently process and analyze whole slide images (WSIs).
CSVtoAnnotations.groovy: Reads coordinates from a CSV file and creates annotations in QuPath at those locations.AnnotationColorMapper.groovy: Applies specific colors to annotations based on their names.CellTypeMaskGenerator.groovy: Generates RGB masks from annotated cell types in WSIs, encoding them in the red channel of an RGB mask.- (Additional script descriptions as needed)
- QuPath (Version 0.4.3)
Clone or download this repository to your local machine.
Each script in this repository is designed to be run within QuPath's script editor. To use a script:
- Open QuPath and load a WSI.
- Open the script editor in QuPath (Automate -> Show script editor).
- Copy and paste the desired script from this repository into the script editor.
- Execute the script.
Contributions to these scripts, including improvements, bug fixes, or additional utility scripts, are welcome. Please feel free to submit pull requests or open issues for discussion.
MIT License - Feel free to use, modify, and distribute these scripts as needed.
- Author: Mohamed Omar, MD
- Email: mao4005@med.cornell.edu
- GitHub: https://github.com/MohamedOmar2020