Welcome to I3D:bio – a research data management resource for bioimaging with a focus on light microscopy
Looking for a resource to:
- learn and teach about microscopy research data management?
- help organize your microscopy research data?
- aid with storing, sharing and archiving your images?
- facilitate linking your image data with experimental protocols and analysis results?
- support setting up microscopy reasearch data management at your institute or facility?
Check out these 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)
Current project status:
What’s new?
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
Meet us at ELMI in Heidelberg!
https://www.embl.org/about/info/course-and-conference-office/events/elmi2025/
Latest Content:
2025-01:
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!
