I3D:bio

@i3dbio@nfdi.social
17 Followers
36 Following
18 Posts
I3D:bio is a DFG-funded project to support research data management for bioimaging data in Germany. The I3D:bio comprises legally independent partners, who collaborate on the project.
Websitehttps://www.i3dbio.de
I3D:bioSep 16, 2024

New papers on BioImaging Research Data Management published!

In May, we contributed to the #JournalOfMicroscopy Special Issue "Light Microscopy Core Facility Management". Our review about implementing #RDM for bioimaging in core facilities:
https://doi.org/10.1111/jmi.13317

Fresh from the press, a discrete use case report about implementing OMERO at the TU Dresden Medical Faculty CFCI is now available in the Journal of Microscopy:
Read the paper by Jannasch et al. here: https://doi.org/10.1111/jmi.13360

I3D:bioSep 12, 2024

Today!! Join Tom Boissonnet (I3D:bio) , Caterina Strambio De Castillia (BINA), and Maria Mirza (EuBI) for their talk about BioImaging Research Data Management (#RDM) hosted through FocalPlane!

4 p.m., CEST, online! Register here:
https://focalplane.biologists.com/2024/08/22/focalplane-features-data-management/

FocalPlane features... data management - FocalPlane

FocalPlane features... data management - News

FocalPlane
I3D:bioMay 7, 2024
Missed the workshop or would like to host a similar workshop on your own?
https://nfdi.social/@nfdi4bioimage/112360641120521720
The workshop material is now available as an open educational resource on Zenodo:
Fuchs, V. et al.: [Workshop] FAIR data handling for microscopy: Structured metadata annotation in OMERO. https://doi.org/10.5281/zenodo.11109616
NFDI4BIOIMAGE (@nfdi4bioimage@nfdi.social)

Attached: 1 image A 2-day intensive workshop on #FAIR data with structured annotations in #OMERO comes to an end. We enjoyed very much the lively & inspiring discussions from & with the participants who created a lovely atmosphere in this online workshop. 🙏 @nfdi4bioimage.bsky.social @i3dbio #OER material to follow.

Nationale Forschungsdateninfrastruktur (NFDI)
I3D:bioApr 30, 2024
NFDI4BIOIMAGEApr 30, 2024
A 2-day intensive workshop on #FAIR data with structured annotations in #OMERO comes to an end. We enjoyed very much the lively & inspiring discussions from & with the participants who created a lovely atmosphere in this online workshop. 🙏 @nfdi4bioimage.bsky.social @i3dbio #OER material to follow.
I3D:bioApr 30, 2024
Thank you from the organizers from both @i3dbio and @nfdi4bioimage to all participants. This was a lot of fun!
https://nfdi.social/@nfdi4bioimage/112360641120521720
NFDI4BIOIMAGE (@nfdi4bioimage@nfdi.social)

Attached: 1 image A 2-day intensive workshop on #FAIR data with structured annotations in #OMERO comes to an end. We enjoyed very much the lively & inspiring discussions from & with the participants who created a lovely atmosphere in this online workshop. 🙏 @nfdi4bioimage.bsky.social @i3dbio #OER material to follow.

Nationale Forschungsdateninfrastruktur (NFDI)
I3D:bioMar 18, 2024

Are you using #OMERO for bioimage data management and want to get more out of your annotations?
Join our workshop about how to leverage structured metadata in OMERO to benefit image analysis and data publication.

Two-day online workshop on April 29th & 30th
Jointly organized by @i3dbio & @nfdi4bioimage
⬇️
https://gerbi-gmb.de/i3dbio/i3dbio-teaching/events-workshops/omero-meta-workshop24/

FAIR microscopy data handling: structured metadata annotation in OMERO - German BioImaging

Workshop Announcement: FAIR data handling for microscopy: Structured metadata annotation in OMERO Location Online, two-day workshop Dates April 29th, 9 a.m. to 4 p.m. and April 30th, 9 a.m. to 3 p.m. Description Microscopy experiments generate information-rich, multi-dimensional data, allowing us to investigate biological processes at high spatial and temporal

German BioImaging
I3D:bioMar 11, 2024
You missed us at #GerBI-GMB Community Meeting in Fulda?
Find here our poster with useful links on microscopy image data management and training material for #OMERO and #metadata. #openaccess #OER #FAIR
https://zenodo.org/doi/10.5281/zenodo.10805203
The Information Infrastructure for BioImage Data (I3D:bio) project to advance FAIR microscopy data management for the community

Research data management (RDM) in microscopy and image analysis is a challenging task. Large files in proprietary formats, complex N-dimensional array structures, and various metadata models and formats can make image data handling inconvenient and difficult. For data organization, annotation, and sharing, researchers need solutions that fit everyday practice and comply with the FAIR (Findable, Accessible, Interoperable, Reusable) principles. International community-based efforts have begun creating open data models (OME), an open file format and translation library (OME-TIFF, Bio-Formats), data management software platforms, and microscopy metadata recommendations and annotation tools. Bringing these developments into practice requires support and training. Iterative feedback and tool improvement is needed to foster practical adoption by the scientific community. The Information Infrastructure for BioImage Data (I3D:bio) project works on guidelines, training resources, and practical assistance for FAIR microscopy RDM adoption with a focus on the management platform OMERO and metadata annotations.

Zenodo
I3D:bioMar 7, 2024
This week, we were at #GerBI-GMB Community Meeting in Fulda discussing bioimage #RDM with the German community of microscopy experts. Thank you for the interest, the exciting exchange about I3D:bio's and our partner project's activities, and the stimulating discussions and ideas from the community.
@nfdi4bioimage #OMERO
I3D:bioJan 22, 2024

#Metadata in #bioimaging is essential for FAIR sharing. And yet the topic can be confusing at times. Many aspects of the why & how of metadata can be overwhelming in the beginning.

Here is a 📽️ overview of structured metadata & (linked) open data in bioimaging:
https://youtu.be/s8AdLmH4E8A?si=lD2iI-FBPqhRGrhf

Susanne Kunis explains technical terms, concepts & what metadata can do to make better science.

What's best: Download the poster from #zenodo to hang it up for your users in your facility
https://zenodo.org/doi/10.5281/zenodo.6821815

Structuring of Data and Metadata in Bioimaging

YouTube
I3D:bioJan 19, 2024
What a pleasure to share work by A. Jannasch et al. https://doi.org/10.1063/5.0182672 These researchers from TU Dresden's Medical Faculty not only share findings about the potential of new pretreatment for bioprosthetic materials for cardiac surgery. What's more, they share large original #bioimaging #histology data + #REMBI annotations in the faculty's #OMERO instance.
The @i3dbio team is excited about the excellent partnership to faclitate OMERO-based RDM, also collaborating with @nfdi4bioimage #FAIR
In vivo application of a glutaraldehyde-free, UVA/riboflavin cross-linked bovine pericardium confirms suitability for cardiovascular substitutes

Glutaraldehyde (GA)-treated bovine pericardium is still the gold standard for the fabrication of bioprostheses needed for the surgical treatment of valvular mal

AIP Publishing