Welcome to I3D:bio – a research data management resource for bioimaging with a focus on light microscopy
Find resources for:
- learning and teaching about microscopy research data management
- helping organize your microscopy research data
- aiding with storing, sharing, and archiving biological images
- facilitating linking bioimage data with experimental protocols and analysis results
- supporting the setup of microscopy research data management at an institute or facility?
Check out the I3D:bio project pages and contact us for questions and support.
I3D:bio is developing the resources, materials and services for the bioimaging community:
- Deployment support for the image data management system OMERO at your institution or university (see Guides & Resources)
- Training for scientists to adopt FAIR image data management practices (see Teaching Material & Events)
- A knowledge-hub about bioimaging RDM (see About Bioimaging Data)
- Teaching bioimaging RDM practices for specific target audiences (see Teaching Material & Events)
- A HelpDesk to respond to your needs and questions regarding bioimaging RDM (see HelpDesk & Contact)
What’s new?
For I3D:bio’s second funding phase, our project partners now start to offer new job openings on the project. Please find current job openings here:
– DKFZ: Project Coordinator position (m/f/d) (Application Deadline: September 9th, 2026)
– GerBI-GMB: RDM Facilitator Bioimaging Community Services (m/f/d) (Application Deadline: September 30th, 2026)
We are excited to announce that the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) has granted funding for I3D:bio 2.0 – the second, consecutive funding phase for this community-centered project on research data management. We are very grateful for the change to continue and extend on the achievements of the first funding phase. We will start the process of hiring new team members and preparing the project kick-off. We will provide more information on the second project phase soon.
Latest Content:
2025-08:
I3D:bio has submitted its proposal to extend the project for a second funding phase to the DFG. The team decided to focus on integrated multi-modal data integration with OMERO (e.g., omics + imaging data), extending the deployment support, and working on more in-depth training material as well as a sustainability strategy to secure the I3D:bio support over the long-term. We welcome new partners in the project: Dr. Jan-Phlipp Mallm and Dr. Ivo Buchhalter from the German Cancer Research Center, and Prof. Dr. Sven Nahnsen from the Quantitative Biology Center (QBiC) in Tübingen. At the same time, we express our sincere gratitude to Dr. Susanne Kunis and Dr. Roland Nitschke for a great collaboration throughout the first funding phase.
2025-08:
I3D:bio presented its work on OMERO deployment at the CoRDI conference. The Conference on Research Data Infrastructures (CoRDI) took place in Aachen on August 26th-28th. The I3D:bio project contributed to CoRDI with a poster about the OMERO deployment strategy. Find the abstract and the poster here: https://doi.org/10.5281/zenodo.16736161
On a second poster, the Trends in Microscopy Data management strategy was presented, to which I3D:bio contributed both in 2023 and in 2025.
2025-07:
I3D:bio conducted an introductory OMERO workshop at the University of Konstanz on the occasion of launching their new instance (supported by I3D:bio).
2025-05:
At this year’s European Light Microscopy Initiative Conference (ELMI 2025) in Heidelberg, I3D:bio will offer two workshops, 1 h each:
- Bioimaging data organization in OMERO
- Hands-on: REMBI-compliant annotations in OMERO
Workshop material is available on Zenodo: https://doi.org/10.5281/zenodo.15639869
2025-03:
I3D:bio and NFDI4BIOIMAGE provided on-site data management using a conference OMERO server at the Trends in Microscopy 2025.
Find more information about TiM 2025 here: https://gerbi-gmb.de/event/tim2025/
The collected data is now moved to a public OMERO server to include data from TiM 2023 and TiM 2025: https://omero-tim.gerbi-gmb.de/webclient/
2024-10:
The I3D:bio team offered a new workshop, directed at teams from imaging facilities and IT departments to learn about a structured approach for implementing a new OMERO instance at a research institution or university. The workshop took place on-premise in Heidelberg on October 16th & 17th. Material is available online:
https://doi.org/10.5281/zenodo.14013026
2024-09:
In collaboration with the TU Dresden Medical Faculty and partners from NFDI4BIOIMAGE, I3D:bio published a use case report about setting up an institutional OMERO instance. See the original paper in Journal of Microscopy: https://doi.org/10.1111/jmi.13360
2024-09:
The Gesellschaft für Biochemie und Molekularbiologie (GBM) hosted the GBM Compact Symposium in Frankfurt on Sept. 26th and 27th.
Jointly organized by NFDI4BIOIMAGE and the I3D:bio project, we presented a workshop about research data management for bioimaging data. Find the workshop material published on Zenodo: https://doi.org/10.5281/zenodo.13861025
2024-05:
Based on the experience with use case partners from I3D:bio, we have published a review: A practical guide to bioimaging research data management in core facilities. Read the full publication in the Journal of Microscopy: Schmidt, C., et al. (2024). Journal of Microscopy, 294, 350–371. https://doi.org/10.1111/jmi.13317
2023-11-28:
Tom Boissonnet offered a workshop on OMERO.figure for the creation of reproducible figures in OMERO at the Halfway to I2K Conference 2023. The workshop recording is now available here.
2023-11-14:
The I3D:bio project has published a key deliverable: The I3D:bio training material as an open, reusable material for local user training by core facility staff and others.
Check out the resource here: https://gerbi-gmb.de/i3dbio/i3dbio-teaching/train-mat/
2023-08-04:
We updated the Bioimaging Metatadata Standards page to integrate the newly published MIHCSME standard by Hosseini et al. Check it out!
