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Extension docs Forum Downloads (latest release) Downloads (all releases)

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 API.

Important!

The use of the web API means that all images are JPEG-compressed. This effectively means it is most useful for viewing and annotating RGB images (including whole slide images), but is not suitable for quantitative analysis where JPEG compression artifacts would be problematic.

Compatibility

The extension is intended for use with QuPath v0.5; it is not compatible with earlier QuPath versions. A new QuPath OMERO extension is currently under active development.

Docs

The main documentation for the extension is at https://qupath.readthedocs.io/en/0.5/docs/advanced/omero.html

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).

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.