https://github.com/qupath/qupath-extension-omero
QuPath extension to work with images through OMERO's APIs
https://github.com/qupath/qupath-extension-omero
Last synced: 2 months ago
JSON representation
QuPath extension to work with images through OMERO's APIs
- Host: GitHub
- URL: https://github.com/qupath/qupath-extension-omero
- Owner: qupath
- License: apache-2.0
- Created: 2024-02-07T13:37:41.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2026-03-23T13:07:13.000Z (2 months ago)
- Last Synced: 2026-03-24T10:12:39.097Z (2 months ago)
- Language: Java
- Size: 3.15 MB
- Stars: 8
- Watchers: 2
- Forks: 2
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
# QuPath OMERO extension
Welcome to the OMERO extension for [QuPath](http://qupath.github.io)!
This adds support for accessing images hosted on an [OMERO](https://www.openmicroscopy.org/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, you can:
* Open the QuPath [extension manager](https://qupath.readthedocs.io/en/latest/docs/intro/extensions.html#managing-extensions-with-the-extension-manager) and install the extension from there (recommended).
* Or download the latest `qupath-extension-omero-[version].jar` file from [releases](https://github.com/qupath/qupath-extension-omero/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](https://qupath.readthedocs.io/en/stable/docs/advanced/omero.html#opening-omero-images)), you need to install the OMERO Java dependencies. This can be done:
* With the [extension manager](https://qupath.readthedocs.io/en/latest/docs/intro/extensions.html#managing-extensions-with-the-extension-manager) by clicking on *Install optional dependencies* when installing the extension (recommended).
* Or by going on the [OMERO download page](https://www.openmicroscopy.org/omero/downloads/), 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/latest/docs/advanced/omero.html.
## Building
You can build the extension using OpenJDK 21 or later with
```bash
./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
```bash
./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.