QuPath BIOP-OMERO extension

Welcome to the BIOP-OMERO extension for QuPath!

This adds support for accessing images hosted on an OMERO server through simple-omero-client API, based on OMERO-ICE API.

The extension is intended for QuPath v0.5.x (at the time of writing). It is not compatible with earlier QuPath versions. However, the 0.7.0 version of this extension is the last compatible one with QuPath 0.4.4.

Documentation

• You can find all the documentation on how to use this extension on our wiki page.
• The JavaDoc of this project is available on the GitHub Page.

Template scripts

• All QuPath-OMERO commands can be used in QuPath scripts (groovy language). Template scripts that make the use of the scripting API are available on our GitHub - qupath-scripts.

Installing

Downloads

• To install the OMERO extension, download the latest qupath-extension-biop-omero-[version].zip file from releases, unzip it and drag the two .jars onto the main QuPath window.

• If you haven't installed any extensions before, you'll be prompted to select a QuPath user directory. The extension will then be copied to a location inside that directory.

• The OMERO-java dependencies are required to make this extension working. Download the .zip file from the OMERO download page, under "OMERO java". Unzip it and copy the libs folder in your extension directory.

WARNING

Due to an unexpected bug in QuPath 0.5.0, the dependencies nested in sub-folder are not read anymore. This bug is now fixed in QuPath 0.5.1.

Update

• You might then need to restart QuPath (but not your computer).

Building

You can build the extension using OpenJDK 17 or later with

gradlew clean build

The output will be under build/libs. You can drag the jar file on top of QuPath to install the extension.