Data Management and Interoperability at Trends in Microscopy 2025
Data management, OMERO, OME-Zarr, and global data sharing were key topics at an event on microscopy data management and hands-on practice at Trends in Microscopy 2025 (#TiM2025), organized by German BioImaging on 17-21st of March 2025, in Münsingen, Germany. We participated in this event, bringing our poster and engaging in valuable discussions on imaging data stewardship, interoperability and data management practices.
Key Highlights from the Event
One of the standout talks was delivered by Matthew Hartley on global image data sharing and the updated BioImage Archive. The updated BioImage Archive is an impressive development that will benefit the whole bioimaging community. Additionally, several hands-on workshops provided in-depth insights into microscopy data management.
1. Data Stewardship in Microscopy Workshop
Led by: Tom Boissonnet, Ksenia Krooß (Heinrich Heine Universität Düsseldorf), and Jens Wendt (University of Münster)
This workshop focused on importing microscopy data into OMERO and the cloud-ready OME-Zarr format. Participants engaged in hands-on metadata annotation using the REMBI methodology, reinforcing best practices in data stewardship.
2. Data Management at France-BioImaging Workshop
Led by: Guillaume Gay (France-BioImaging)
This session explored the “Investigation, Study, Assay” hierarchy implemented at France-BioImaging and the increasing role of semantic web technologies in structuring and linking imaging datasets across research infrastructures.
3. OMERO-metrics: Quality Control at the Microscope Workshop
Led by: Julio Mateos Langerak (CNRS)
This workshop introduced OMERO-metrics, a web application designed to leverage OMERO’s data management capabilities for standardizing metrology analysis procedures. The tool provides an intuitive dashboard for Imaging Core Facilities to enhance quality assessment workflows in microscopy.
TiM2025 and On-Site FAIR Data Management
At the conference, the I3D:bio team provided an OMERO-based framework for on-premise FAIR data management throughout the meeting. Conference participants and workshop providers were invited to collaborate in an on-site test case, applying FAIR data principles across different imaging modalities and image analysis approaches. The TiM-OMERO server facilitated seamless data access, with images available via APIs and directly from a fileshare on a HIVE.
The impact of this initiative was significant: 220 imaging scientists, a dedicated team of data stewards, state-of-the-art microscopy setups, and committed industry teams worked together to generate an impressive 2.6 TB of annotated image data (1395 files) in OMERO! Annotation is still ongoing (written on 24th of March 2025), and the image data will soon be available for reuse here.
Towards an Interoperable Future
Throughout TiM2025, discussions on metadata standards, image data interoperability, and global sharing underscored the growing importance of these challenges for the imaging community. At foundingGIDE, we are committed to integrating these insights into our work, fostering collaboration, and advancing solutions that support an open and interoperable bioimaging ecosystem.
Stay tuned as we continue to engage with the global imaging community to drive progress in data management and interoperability!