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:

Current project status:

What’s new?

2025-08: I3D:bio will present its work on OMERO deployment at the CoRDI conference

The Conference on Research Data Infrastructures (CoRDI) takes place in Aachen on August 26th-28th. The I3D:bio project will contribute to CoRDI with a poster about the OMERO deployment strategy.
Find the abstract here: https://doi.org/10.5281/zenodo.16736161

On a second poster, the Trends in Mircroscopy Data management strategy is presented, to which I3D:bio contributed both in 2023 and in 2025. 

Information about CoRDI 2025: https://www.nfdi.de/cordi-2025/

Latest Content:

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!