PUBLIC ARCHIVE

This repo is now archived and its content has been integrated into the QuPath-BIOP extension in order to avoid complexity with catalog installation. This repo will no longer be maintained. Scripts are now accessible under Extensions -> BIOP -> scripts

Please consider using the QuPath-BIOP extension instead to benefit from latest scripts / fixes

QuPath Scripts

This repository contains Scripts we found useful when using QuPath.

They are intended for use with the latest version of QuPath and perhaps require extra dependencies. All dependencies are written inside the header of each script.

Note

The main branch contains only scripts that are compatible with the latest version of QuPath (i.e. QuPath 0.6.x). If you are using an older version of QuPath (i.e. QuPath 0.5.x), please checkout the corresponding branch

How to use scripts

• Clone this repository on your computer
• Open QuPath, enter preferences (Edit -> Preferences -> Scripting) and add the path to the qupath-scripts repo
• Before running any script, you will need to have an image open in QuPath.
• On QuPath, go under Automate -> Shared script.
• Click on the script you want.
• Read the small headers = REQUIREMENTS = and = TO MAKE THE SCRIPT RUN = to know what should be configured on the image to make the script run.
• Click on run->run.