QuPath Groovy Scripting Guide

This repository contains a guide on how to use Groovy code in QuPath for automation and customization purposes. QuPath offers a built-in script editor that allows you to write and run Groovy scripts to perform various tasks and extend the functionality of the software.

Installation

1. Clone this repository to your local machine.
2. Follow the official QuPath installation guide to set up QuPath on your computer.

Usage

Running Groovy Scripts in QuPath

1. Open the QuPath application.
2. Load your images and annotations into QuPath.
3. Navigate to Automate > Show script editor in the menu bar to open the script editor.
4. Write or paste your Groovy script into the script editor. You can also load an existing script using the File > Open... option in the script editor.
5. Save your script (optional) using the File > Save as... option in the script editor.
6. Run your script by clicking the Run button in the script editor. You can also use the Ctrl+R (or Cmd+R on macOS) keyboard shortcut to run the script.

Example Groovy Script

The following is an example Groovy script that prints the names of all the images currently open in QuPath:

import qupath.lib.projects.Project
import qupath.lib.images.ImageData

Project project = qupath.getProject()
List<ImageData> imageDataList = project.getImageList()

imageDataList.each { imageData ->
    println "Image name: ${imageData.getServer().getMetadata().getName()}"
}

Copy and paste this script into the QuPath script editor and run it to see the output.

Acknowledgements

• Exporting images with QuPath
• Exporting annotations with QuPath
• Json Annotation: Sharing annotated QuPath files with other users

Contributing

If you'd like to contribute to this project, please create a fork of this repository, make your changes, and submit a pull request.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Support

For any questions or issues, please use the QuPath forum or open an issue in this repository.