Boosting Biodata Bootcamp 2026, Workshop #6: Research Data Management for Microscopy – OMERO

These are the presentation slides for the Workshop #6 "Research Data Management for Microscopy – OMERO" for the conference Boosting Biodata Bootcamp in Aachen 15. - 17.09.2026.

The aim of the workshop was to familiarize members of adjacent NFDI consortia with the concept and capabilities of the prevalent RDM platform for microscopy image data, OMERO.

This introductory workshop provides an overview of OMERO, the open-source image data management platform most used in the field of bioimaging. Participants will learn about the origins and structure of OMERO and gain a better understanding how image data is handled, annotated and accessed in OMERO.

The workshop covers the following topics:

• Background & Origins: A brief look at the OME project and how OMERO fits into the landscape of research data management for bioimaging.

• The OMERO Web Interface: A guided tour of OMERO.web, exploring its layout, navigation, and core capabilities.

• Data Structure in OMERO: Understanding how image data is organized using the Project–Dataset–Image hierarchy and how groups and permissions work.

• Importing & Exporting Data: How to get image data into OMERO and how to retrieve or download data from the platform.

• Interacting with Image Data: Exploring ways to visualize and utilize images within OMERO. Showcasing the integration with third-party tools such as Fiji/ImageJ, QuPath or Python scripts.

• Metadata & Annotations: How OMERO captures and preserves metadata, and how users can enrich their data using tags, key-value pairs, file attachments.

Target Audience: BioData users who are interested in how FAIR RDM can be handled for image data, BioData users who want to learn more about how to interface with image data on OMERO, BioData users who want to learn about metadata (annotation) of microscopy-based image data.

We acknowledge funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI 46/1 – 501864659.