https://github.com/qupath/qupath-extension-omero-web

QuPath extension to work with images through OMERO's web API
https://github.com/qupath/qupath-extension-omero-web

Last synced: 2 months ago
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QuPath extension to work with images through OMERO's web API

• Host: GitHub
• URL: https://github.com/qupath/qupath-extension-omero-web
• Owner: qupath
• License: gpl-3.0
• Created: 2021-06-02T14:02:57.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2024-05-31T10:12:46.000Z (8 months ago)
• Last Synced: 2024-05-31T11:31:28.124Z (8 months ago)
• Language: Java
• Homepage:
• Size: 394 KB
• Stars: 8
• Watchers: 5
• Forks: 12
• Open Issues: 9
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE.md

Awesome Lists containing this project

README

        
[![Extension docs](https://img.shields.io/badge/docs-qupath_omero-red)](https://qupath.readthedocs.io/en/stable/docs/advanced/omero.html)

[![Forum](https://img.shields.io/badge/forum-image.sc-green)](https://forum.image.sc/tag/qupath)

[![Downloads (latest release)](https://img.shields.io/github/downloads-pre/qupath/qupath-extension-omero/latest/total)](https://github.com/qupath/qupath-extension-omero/releases/latest)

[![Downloads (all releases)](https://img.shields.io/github/downloads/qupath/qupath-extension-omero/total)](https://github.com/qupath/qupath-extension-omero/releases)

# 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 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](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).

## Building

You can build the extension using OpenJDK 17 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.