QuPath OMERO extension

Welcome to the OMERO extension for QuPath!

This adds support for accessing images hosted on an OMERO server through OMERO's web (and other) API.

The extension is intended for QuPath v0.6 and later. It is not compatible with earlier QuPath versions.

Installing

To install the OMERO extension, download the latest qupath-extension-omero-[version].jar file from releases and drag it 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.

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

If you want to use the ICE pixel API (see the documentation), you need to install the OMERO Java dependencies: on the OMERO download page, under "OMERO Java", download the .zip file, unzip it and copy the libs folder in your extension directory.

Documentation

The main documentation for the extension is at https://qupath.readthedocs.io/en/stable/docs/advanced/omero.html.

Building

You can build the extension using OpenJDK 21 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.

Running tests

You can run the tests with

./gradlew test

Some of the tests require having Docker installed and running.

By default, a new local OMERO server will be created each time this command is run. As it takes a few minutes, you can instead create a local OMERO server by running the qupath-extension-omero/src/test/resources/server.sh script and setting the OmeroServer.IS_LOCAL_OMERO_SERVER_RUNNING variable to true (qupath-extension-omero/src/test/java/qupath/ext/omero/OmeroServer file). That way, unit tests will use the existing OMERO server instead of creating a new one.