🧾QuPath Script

QuPath Script explanation

1. Under Automate open the script editor, copy the script present here, and make changes in the marked sections accordingly. Depending on which tissue detection was performed choose the according script provided.

GitHub files, showing the different scripts and the README file

1. The .groovy file is the script and can be downloaded and opened in Qupath under Automate > Script Editor > File > Open. Alternatively, the raw script can be copied () from the github and pasted into a new script file in QuPath.

Explanation of the manual tissue detection script

1. Within the .groovy script for QuPath, it is visible in //comment where you need to add the lines saved in your personal scripts. It is also indicated from which Script you need to copy the lines over.

2. If you have only one Region you want to analyse, the components 2-4 can be deleted from the script as indicated.

Open the downloaded script in QuPath. Then under file>open, open up the scripts you have created for your project (EstimateStainVectors, CellDetection). Then replace the lines marked in the BatchAnalysis_Scipt script with your lines of script by copying them across.