@nfdi4bioimage
NFDI4BIOIMAGE, a consortium of the NFDI in Germany, is a legally non-independent collaboration project. It focuses on research data management for bioimaging and image analysis. The consortium does not act autonomously towards third parties.
In our recent blog post, Cornelia Wetzker shares, how she led a project to make bioimage data from fluorescence lifetime imaging microscopy more #fair. She created a plugin for the open-source 3D viewer #Napari that enables the import and analysis of FLIM data.
👉 nfdi4bioimage.de/en/news/meet...
Rodrigo Escobar Díaz Guerrero presented at the Workshop "Data Management for Chemometrics and Quality Control" a solution to bridge different data sources: #LEO, a web-based platform to link metadata sources with image servers like #OMERO.
👉 Find out more in his preprint: arxiv.org/abs/2508.00654
Mohsen Ahmadi presents his poster, "FAIR bioimaging data management workflow for plasma medicine by integrating #OMERO, eLabFTW, and Adamant via #Jupyter notebook," at the annual meeting of the @researchdataall.bsky.social (#rdade2026).
👉 Find out more about the workflow: zenodo.org/records/1845...
A photo of Michele Bortolomeazzi standing in front of a seminar room giving a presentation.
Find OMERO training material for reuse:
👉 zenodo.org/communities/...
👉 zenodo.org/communities/...
Honoring the Love Data Week 2026, Michele Bortolomeazzi and Christian Schmidt from @nfdi4bioimage.bsky.social organized a workshop on bioimage data management using #OMERO at the @dkfz.bsky.social. It was based on the training material developed throughout the course of NFDI4BIOIMAGE and I3D:bio.
🌟 #MeetOurDataStewards #7: Cornelia Wetzker
Although processing and analyzing multidimensional data sets can be quite demanding, it is important to conduct research in a #FAIR manner. If you need help with data handling, feel free to contact our data stewards.
👉 nfdi4bioimage.de/help-desk/
Join the online lecture "Open Science, Open Data & KonDATA - Publishing research data sustainably and making it accessible" by our @nfdi4bioimage.bsky.social data steward Maximilian Müller on February 11 at 1:00 pm as part of the Love Data Week 2026.
👉 www.kim.uni-konstanz.de/kim-news/new...
@nfdi4bioimage.bsky.social researcher Carsten Fortmann-Grote and his colleague Kristian Ullrich (both MPI EvolBio) presented @mpi-evolbio.bsky.social's data management concept and adaptations for the platform at the openBIS User Group Meeting 2025.
To the presentation:
👉 doi.org/10.5281/zeno...
🌟#MeetOurDataStewards #7: Cornelia Wetzker
Cornelia can help you with requests regarding research data management in general, #bioimage data handling and management e.g. in the platform #OMERO and publication in public repositories.
👉 nfdi4bioimage.de/about-us/dat...
Welche Rolle hat #NFDI eigentlich in der #EOSC Association? Darum geht es in unserer brandneuen Podcast-Folge. 🎧
Jetzt hören:
▶️ Spotify: open.spotify.com/episode/6jN3...
▶️ Acast: shows.acast.com/nfdi-podcast...
▶️ Youtube: www.youtube.com/watch?v=GHMx...
#fdm #rdm #forschungsdaten
🎉 The 2026 edition of our @nfdi4bioimage.bsky.social calendar focuses on repositories for the publication of bioimage datasets. The first entry is dedicated to the BioImageArchive, and the accompanying image is by Sarah Knapp (RWTH Aachen University).
Read more:
👉 nfdi4bioimage.de/resources-an...
19th #OME Community Meeting, Düsseldorf · 28–30 April 2026
Registration is now open! Join researchers, developers, and imaging facility staff to connect, share experiences, and discuss the future of OME tools.
Details & registration (deadline: 31 March 2026):
gerbi-gmb.de/event/ome-20...
Get an insight of the #RDM4Mic meeting, which took place in Münster from October 21 to 23, 2025, on YouTube now. Here you will find ten presentations on various topics related to research data management:
👉 www.
youtube.com/watch?v=pSr0OwLD-qY&list=PL2k-L-zWPoR67_02CuEROsYr1nnCNgMcI
Winter-themed graphic titled “Winter Data Wonder #11.” A dark blue text panel framed by snow and icicles reads: “NFDI4BIOIMAGE shows how even a 100-GB microscopy dataset can be accessed directly on a smartphone — thanks to data streaming with the cloud-compatible OME-Zarr format.” Light blue snowy background with falling snow dots and a small snow-covered tree in the lower right corner.
❄️Winter Data Wonder #11
NFDI4BIOIMAGE shows how cloud-compatible data streaming makes large image datasets directly viewable in the browser — enabling mobile, flexible work with microscopy data.
🔗 Read more:
nfdi4bioimage.de/news/news-de...
Contributed by @nfdi4bioimage.bsky.social
@nfdi4bioimage.bsky.social started the new year with enthusiasm and many plans, and you'll find what's new, what's upcoming, and what's to read or review in our newsletter.
📨 nfdi4bioimage.de/community-in...
Would you like to stay informed about #NFDI4BIOIMAGE?
👉 nfdi4bioimage.de/community-in...
Researchers in the #BiologicalSciences and #AgricultureSciences, who work with image data and want to improve their data management workflows, can now access the material from the workshop on "Image Data Management in the Biological Sciences and Agricultural Research."
📚 doi.org/10.5281/zeno...
NFDI4BIOIMAGE from A to Z. Z as in Zenodo. Zenodo is a general-purpose data repository built on open source software that accepts all forms of research output from data files to presentation files. It was developed by the European Organization for Nuclear Research (CERN), but is open to researchers from outside the EU. Data is stored in the CERN Data Center, which provides long-term preservation. Source: https://datamanagement.hms.harvard.edu/share-publish/data-repositories/zenodo
#NFDI4BIOIMAGEfromAtoZ - Z as in Zenodo
For us as a consortium committed to helping others make their data #FAIR, Zenodo is a useful platform where we make presentations, training materials, posters, and papers publicly available for everyone.
Find our materials here:
👉 zenodo.org/communities/...
#NFDI4BIOIMAGEfromAtoZ - Y as in YAML
If your research involves lots of files and metadata, YAML can help you structure everything clearly and transparently. This text-based format can be used to describe image metadata and analysis parameters in a human-readable and machine-processable way.
NFDI4BIOIMAGE from A to Z: X as in XML. Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. Source: https://en.wikipedia.org/wiki/XML
#NFDI4BIOIMAGEfromAtoZ - X as in XML.
Encouraging the use of standards like XML is important to @nfdi4bioimage.bsky.social, as it guarantees interoperability between softwares and labs.
More about the specific file format OME-XML for biological image data:
👉 docs.openmicroscopy.org/ome-model/5....
#NFDI4BIOIMAGEfromAtoZ - W as in Workflow
If your research involves working with large amounts of data, it is important to plan your data workflow beforehand. A planned #workflow makes your data easy to process and reproduce, from the first image to publication.
NFDI4BIOIMAGE from A to Z. U as in Usability. Usability, or user friendliness, describes how effectively a system supports users in completing intended tasks with a high level of safety, efficiency, and reliability, while promoting a smooth and intuitive workflow. Applied to research data, usability refers to how easily other people (or even your future self) can find, understand, access, and correctly use the data.
#NFDI4BIOIMAGEfromAtoZ - U as in Usability.
Usability is closely linked to the #FAIR data principles that we at @nfdi4bioimage.bsky.social strive for. To improve the usability of your data, you need to document it well, add metadata and store data in common, non-proprietary formats.
#NFDI4BIOIMAGEfromAtoZ - T as in TIFF
When working with microscopy data, you often need image formats that preserve every detail of your measurements. #TIFF (Tagged Image File Format) is a raster image format particularly suited for high-quality, multidimensional microscopy data.
#NFDI4BioImageFromAtoZ - S for semantic annotation
Would you like to create #FAIR bioimage data with your research? Then, you can’t ignore semantic annotation: Data only becomes reusable, interoperable, and thus FAIR, through standardized annotation using shared vocabularies and ontologies.
NFDI4BIOIMAGE from A to Z: R as in REMBI. Recommended Metadata for Biological Images (REMBI) provides guidelines for metadata for biological images to enable the FAIR sharing of scientific data. REMBI is the result of the bioimaging community coming together to develop a metadata checklist to describe the imaging data itself, together with supporting metadata such as those describing the biological study and sample. It will also help enable automated data harvesting leveraging machine accessibility. Source: https://www.ebi.ac.uk/bioimage-archive/rembi-help-overview/
#NFDI4BIOIMAGEfromAtoZ - R as in REMBI.
REMBI was developed by the light, electron, and X-ray microscopy communities to increase the likelihood that image data will be reused by their own reserachers, but also by other users of archived image material.
Read more:
👉 www.nature.com/articles/s41...
NFDI4BIOIMAGE from A to Z: Q as in QUAREP-LiMi. QUAREP-LiMi (Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy) is an international initiative with a multifaceted aim to enhance the quality, reliability, and reproducibility of light microscopy data across the life and material sciences. Source: https://quarep.org/about/
#NFDI4BIOIMAGEfromAtoZ - Q as in QUAREP-LiMi.
Quarep-LiMi is one of @NFDI4BIOIMAGE's partners with whom we exchange regularly and work together to develop internationally coordinated standards and processes for quality controll and assessment.
Have a look at the initiative:
👉 quarep.org
#NFDI4BIOIMAGEfromAtoZ - P as in Pixels.
In biological microscopy, #pixels are more than just image dots – they are quantitative measurements that encode spatial and intensity information at the core of high-dimensional bioimaging data.
#NFDBIOIMAGEfromAtoZ - O for OMERO.
What do @nfdi4bioimage.bsky.social and the @openmicroscopy.org have in common? Both aim to improve the management, documentation, and sharing of bioimage data.
👉 Find out more about #OMERO: www.openmicroscopy.org/omero/
#NFD4BIOIMAGEfromAtoZ - N as in NFDI
Since 2020, @nfdi.de has been working with 26 consortia and Base4NFDI toward its vision of “data as a common good for excellent research, organized by the scientific community in Germany.” In 2023 @nfdi4bioimage.bsky.social joined the NFDI. 👉 www.nfdi.de?lang=en
NFDI4BIOIMAGE A-Z. M as in Metadata Standards. Community-driven metadata checklists make it easier for third-party users of original data to understand the dataset. Such standards depend on the research field and the technology used. Peer groups and communities of specialists determine what information is important and should always accompany publicly available data. (https://gerbi-gmb.de/i3dbio/i3dbio-resources/metadata-guide/)
#NFDI4BIOIMAGEfromAtoZ - M as in Metadata Standards.
Standards developed by the bioimaging community emphasize that metadata should contain information relevant to microscopists, computer vision researchers, and imaging scientists - e.g. the imaging method.
👉 gerbi-gmb.de/2024/12/05/m...
Graphic showing the NFDI4BIOIMAGE A-Z logo and five creative commons lincensing stickers. The text reads: L as in License. Legal instrument that defines the terms under which research data can be accessed, used, and shared. Published research data have limited potential for re-use if re-use is not clearly defined. It is, therefore, crucial to assign a license to a dataset. Community standards and good scientific practice should still be observed even if not enforced by licenses. (Link: https://rdm.mpdl.mpg.de/after-research/licenses/)
#NFDI4BIOIMAGEfromAtoZ - L as in License.
An important aspect of making your research data #FAIR is to make it #reusable.
We at @NFDI4BIOIMAGE encourage you to make your data publicly available under an appropriate license to increase its potential for reuse.
