https://github.com/mohamedomar2020/qupath_scripts
Custom groovy scripts for QuaPath
https://github.com/mohamedomar2020/qupath_scripts
celltype-annotation digital-pathology groovy-script masked-image-modeling qupath qupath-script
Last synced: 3 months ago
JSON representation
Custom groovy scripts for QuaPath
- Host: GitHub
- URL: https://github.com/mohamedomar2020/qupath_scripts
- Owner: MohamedOmar2020
- License: mit
- Created: 2024-01-22T14:26:49.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2024-01-22T14:44:51.000Z (about 1 year ago)
- Last Synced: 2024-10-10T02:42:24.349Z (7 months ago)
- Topics: celltype-annotation, digital-pathology, groovy-script, masked-image-modeling, qupath, qupath-script
- Language: Groovy
- Homepage:
- Size: 8.79 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# QuPath Helper Scripts
## Overview
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).
## Scripts Included
- `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)
## Prerequisites
- [QuPath](https://qupath.github.io/) (Version 0.4.3)
## Installation
Clone or download this repository to your local machine.
## Usage
Each script in this repository is designed to be run within QuPath's script editor. To use a script:
1. Open QuPath and load a WSI.
2. Open the script editor in QuPath (Automate -> Show script editor).
3. Copy and paste the desired script from this repository into the script editor.
4. Execute the script.
## Contributing
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.
## License
[MIT License](LICENSE) - Feel free to use, modify, and distribute these scripts as needed.
## Contact
- Author: Mohamed Omar, MD
- Email: [email protected]
- GitHub: https://github.com/MohamedOmar2020