Whole slide and microscopy image analysis with QuPath and OMERO

TL;DR

This paper introduces an extension for QuPath that allows it to access images and metadata from OMERO servers, enabling efficient analysis of large, remote bioimages and facilitating integration with other image management systems.

Contribution

The paper presents a new extension that connects QuPath to OMERO, enhancing its capability to handle remote large-scale bioimages and serving as a template for further integrations.

Findings

Enables QuPath to access images from OMERO servers

Improves efficiency in analyzing large remote images

Provides a template for connecting bioimage analysis tools

Abstract

QuPath is open-source software for bioimage analysis. As a desktop application that is flexible and easy to install, QuPath is used by labs worldwide to visualise and analyse large and complex images. However, relying only on images stored only on a local file system limits QuPath's use for larger studies. This paper describes a new extension that enables QuPath to access pixels and metadata from an OMERO server. This enhances the software by allowing it to work efficiently with images stored remotely, while also serving as a template for developers who want to connect QuPath to other image management systems.