petebankhead/qupath-extension-omero

QuPath extension to work with images through OMERO's APIs

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.

Important!

By default, this extension uses the OMERO web API to read images, which has several limitations. See the Reading images section.

The extension is intended for QuPath v0.5 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).

Reading images

The extension uses several APIs to read images:

• The OMERO web API. This method is enabled by default and available on every OMERO server. It is fast but only 8-bit RGB images can be read, and they 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.
• The OMERO Ice API. This method can read every image and access raw pixel values. However, you have to install the OMERO Java dependencies to enable it: from the OMERO download page, under "OMERO Java", download the .zip file, unzip it and copy the libs folder in your extension directory. Note that it is not possible to use the Ice API when accessing an OMERO server with a guest account, you have to be authenticated.
• The OMERO Pixel Data Microservice (available here). If this microservice is installed on your OMERO server, the extension will automatically detect it. If that's not the case, check that the port indicated in the settings of the extension corresponds to the port used by the microservice on the OMERO server (by default 8082). This API can read every image and access raw pixel values.

Scripting

Script examples are located in the sample-scripts folder. They show how the extension can be used from scripts (with or without the graphical user interface).

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.