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.

OMERO scripts

Under QuPath folder, you will find scripts to get an instance of OMERO and communicate with it.

Dependencies and installation

To make scripts work, you will need three dependencies :

• simple-omero-client
• qupath-extension-biop-omero
• OMERO.java

For simple-omero-client, download the latest version of simple-omero-client-[version].jar and copy it in the folder C:\QuPath_Common_Data_0.3\extensions

For the last two dependencies, look at the readme of qupath-extension-biop-omero to know how to install.

How to use scripts

• All the necessary methods to communicate with OMERO from QuPath are available under the static class OmeroRawScripting.
• Before running any script, you will need to have an image, coming from OMERO, open in QuPath.
• On QuPath, go under Automate -> Shared script -> OMERO.
• 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.