NFDI4BIOIMAGE

Last week, the communications managers from all @NFDI@nfdi.social consortia met in Mainz to exchange best practices and discuss joint campaigns. 👀

Jana Bendigs attended the meeting together with Inga Mohr and led a workshop on the #evaluation of #sciencecommunication.

We would like to express our thanks for the excellent organization, the pleasant atmosphere, and the stimulating discussions, as well as to @nfdi4culture@nfdi.social, @NFDI4Memory@nfdi.social and @NFDI4Chem@nfdi.social for the organization.

Yesterday, our coordinators Inga Mohr and Christian Schmidt represented @nfdi4bioimage@nfdi.social at the @NFDI@nfdi.social Management Präsenztreffen at Akademie der Wissenschaften und der Literatur | Mainz.

A big thank you goes to @nfdi4culture@nfdi.social @NFDI4Memory@nfdi.social and @NFDI4Chem@nfdi.social for the organization and invitation.

#OneNFDI

Data Steward Vanessa Fuchs held an interactive workshop on “Imaging data management with #OMERO” at the fourth FDM-Werkstatt, organised by @fdm_nrw@nfdi.social in cooperation with the RDM Competence Centre of University of Düsseldorf, CEPLAS - Cluster of Excellence on Plant Sciences, @nfdi4plants@nfdi.social and @nfdi4bioimage@nfdi.social, last week.

Find her slides here
👉 https://doi.org/10.5281/zenodo.19352621

To the workshop material:
📔 https://doi.org/10.5281/zenodo.19366801

The Euro-BioImaging Image Data Community Days are still in full swing through tomorrow, featuring presentations, hands-on workshops, and networking events focused on image data.
We thank @eurobioimaging@bird.makeup for the invitation to contribute to this wonderful event, and all the participants for the lively discussions and exchange.

At the Chemnitz #Linux Days, Michael Scherle and Rafael Gieschke presented the current status of the VDI for #OpenStack project. This project aims to develop a VDI based open source technology with the goal of creating a comprehensive IT toolkit that promotes digital sovereignty.

👉 Watch the video: https://media.ccc.de/v/clt26-417-open-source-vdi-hw-beschleunigter-remote-access-zu-libvirt

👉 Get the slides: https://chemnitzer.linux-tage.de/2026/media/programm/folien/417.pdf

👉 Find out more about the project: https://nfdi4bioimage.de/en/news/presenting-the-nfdi4bioimage-driven-vdi-service-at-clt-2026/

Our NFDI4BIOIMAGE Summer Newsletter is now available! 🎉

Recently published, it provides updates on news, upcoming events and noteworthy articles and reviews from the bioimaging community.

Further information about the newsletter and the registration you can find here: https://nfdi4bioimage.de/en/news/newsletter/

What's new in Ome-Zarr 0.6?

Ome-Zarr is a cloud-optimised next-generation file format #NGFF for bioimaging, aiming to increase #FAIR access and remove barriers in the scientific process. The latest version offers numerous improvements and new features.

👉 Find the presentation on Zenodo: https://doi.org/10.5281/zenodo.19335305

It’s all about #FAIR data.

The presentation "Developing Towards the Ideal FAIR Research Data Management Environment," given by Johannes Soltwedel, Tom Boissonnet, and Stefanie Weidtkamp-Peters at the @GerBI@mstdn.science community meeting on March 17, 2026, clearly demonstrates this.

The presentation provides an update on recent developments aimed at improving the #ResearchDataManagement environment for researchers, microscopists, and bioimage analysts.

👉 Find out more: https://zenodo.org/records/19063027

OME-Zarr: From Idea to Standard and Beyond?

Today, we would like to share with you the presentation slides developed by
@joshmoore@fediscience.org for a talk in the bioimaging North America: Insights and Educational Tools from Industry Series.

The presentation looks back at the early days of the Open Microscopy Environment (#OME) and highlights ongoing challenges related to data access, metadata and reproducibility.

👉 Find the presentation on zenodo: https://doi.org/10.5281/zenodo.20275730

🗓️ New month, new image in the NFDI4BIOIMAGE wall calendar.

This time, we’re featuring microscopic images of cells with drug-induced phospholipidosis.

This publication marks the first collaboration between an @nfdi4bioimage@nfdi.social Data Steward and the Image Data Resource. Our expert Jens Wendt handled a significant portion of the upload and annotation process, making the data not only available but also directly searchable, interactive, and reusable. 🔬

👉 Explore the data: https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2282

#NFD4BIOIMAGEfromAtoZ - N as in NFDI

Since 2020, the German National Research Data Infrastructure @NFDI@nfdi.social has been working with 26 consortia and the Base4NFDI network toward its vision of “data as a common good for excellent research, organized by the scientific community in Germany.” In 2023, @nfdi4bioimage@nfdi.social joined the NFDI as one of eight life science consortia, alongside @nfdi4plants@nfdi.social @FAIRagro@nfdi.social @nfdi4immuno@nfdi.social @ghga@genomic.social @nfdi4biodiv@bird.makeup @NFDI4Microbiota@nfdi.social and @nfdi4health@nfdi.social.

👉 https://www.nfdi.de/?lang=en

📅 Investigating in vivo tumor metabolismin in the @nfdi4bioimage@nfdi.social wall calendar in June 2026

This image by Dario Livio Longo of the Institute for Biostructures and Bioimaging at the Italian National Research council shows the quantification of glucose consumption in a mouse model of breast cancer using magnetic resonance imaging (#MRI).

👉 Click here for the study: https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/nbm.4602

👉 Here you can find the dataset: https://eubi-xnat.hpc4ai.unito.it/app/template/XDATScreen_report_xnat_projectData.vm/search_element/xnat:projectData/search_field/xnat:projectData.ID/search_value/glint_glucose-3OMG

@nfdi4bioimage@nfdi.social researcher Carsten Fortmann-Grote and his colleague Kristian Ullrich (both MPI EvolBio) presented the data management concept of the Max Planck Institute for Evolutionary Biology and their adaptations for the platform at the openBIS User Group Meeting 2025. They also reported on their experiences with installation and service management and suggested improvements for openBIS that should be taken into account in future development work.
To the slides:
👉 https://doi.org/10.5281/zenodo.17191503

🌟 #MeetOurDataStewards #8: Cornelia Wetzker

Conni organizes workshops that teach scientists and staff the concepts of #ResearchDataManagement in bioimaging. While guidelines and policies are increasingly being implemented, the real challenge for researchers lies in translating #FAIR principles into their daily research practices and applying them sustainably.

👉 @nfdi4bioimage@nfdi.social publish numerous #RDM workshop materials on Zenodo.
Feel free to take a look: https://zenodo.org/communities/nfdi4bioimage/records?q=&l=list&p=1&s=10&sort=newest

🌟 MeetOurDataStewards

In our recent blog post, Cornelia Wetzker shares, how she led a project to make bioimage data from fluorescence lifetime imaging microscopy (FLIM) more #fair. In close collaboration with her @nfdi4bioimage@nfdi.social colleagues and others, she created a workflow and a plugin for the open-source 3D viewer #Napari that enables the import and analysis of FLIM data.

👉 Learn more about the project and find inspiration to contribute to similar work: https://nfdi4bioimage.de/en/news/meet-our-data-stewards-cornelia-wetzker/

Practical Implementation of FAIR Bioimaging Workflows in Plasma Medicine

At the 5th Workshop on FAIR Data in #PlasmaScience (FDPS-V) at @ruhr-uni-bochum.de, @mohsenahmadi@nfdi.social presented his work integrating research data management systems for #bioimaging in plasma medicine with Jupyter Notebook workflows. His presentation highlighted practical strategies to support #FAIR and interoperable bioimaging data handling in plasma medicine research.

👉 Find out more: https://www.biorxiv.org/content/10.64898/2026.01.26.700509v1.full

In microscopy research, a primary data management challenge is integrating large datasets stored across different platforms.

Rodrigo Escobar Díaz Guerrero presented at the Workshop "Data Management for Chemometrics and Quality Control 2026" 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

Boosting Biodata Bootcamp 2026 🎈

If you are looking forward to the Boosting Biodata Bootcamp #BBB, which will be held at RWTH Aachen University from 15 to 17 September 2026, you can now view the available workshops, the event schedule, and submit an abstract.

👉 Abstract submission: https://lnkd.in/d_pB-TeP
👉 Registration opens on 15 May at https://lnkd.in/dsZYYHbR

@NFDI4Microbiota@nfdi.social is hosting the conference in collaboration with @FAIRagro@nfdi.social, @nfdi4plants@nfdi.social @nfdi4biodiv@bird.makeup and @nfdi4bioimage@nfdi.social

🗓️ New Picture in the @nfdi4bioimage@nfdi.social Wall Calendar

What happens to large imaging datasets once a project ends?

This was the questions facing Katrín Möller at the University of Iceland. Together with Isabel Kemmer, data steward at Euro-BioImaging, she deposited the dataset in the #BioImageArchive. They carefully guided this process to ensure that the data was curated and stored according to #FAIR principles.

👉 Find out more: https://nfdi4bioimage.de/en/community/wall-calendar/wall-calendar-2026/#Apr2026

Are you at your wits’ end when it comes to making your #BioImage data available and archiving it? Fortunately, you’re not alone!

The poster, "Help Desk for Community Support in Bioimage Research Data Management," presented at the 2026 @GerBI@mstdn.science Community Meeting by @nfdi4bioimage@nfdi.social data stewards Cornelia Wetzker, Maximilian Müller, and Vanessa Fuchs, outlines the help desk's services and strategies to make bioimage data more #FAIR throughout the research data life cycle.

👉 https://doi.org/10.5281/zenodo.19107804

📆 Mark your calendars for the #EuroBioimaging Image Data Community Days taking place from April 13 to 17, 2026.

Our @nfdi4bioimage@nfdi.social colleagues Michele Bortolomeazzi and Christian Schmidt (both @DKFZ@helmholtz.social) will host the workshop session "Process management for the institutional deployment of OMERO as an image data RDM platform" on April 13 at 3:00 pm and provide deeper insights into the #OMERO implementation process.

Register here for the session:
👉 https://docs.google.com/forms/d/e/1FAIpQLScmdLlR25v2tc_SseW8Is5h3vOkNbyQ1mXpk6qj55A2O_V3Dg/viewform

Honoring the Love Data Week 2026, Michele Bortolomeazzi and Christian Schmidt from @nfdi4bioimage@nfdi.social organized a workshop on bioimage data management using OMERO at their home institution, the @DKFZ@helmholtz.social in Heidelberg.
The workshop was based on the training material developed throughout the course of NFDI4BIOIMAGE and I3D:bio.

Check out the Zenodo Communities to find #OMERO training material for reuse:
👉 https://zenodo.org/communities/nfdi4bioimage/
👉 https://zenodo.org/communities/i3dbio/

💥 #MeetOurDataStewards: Why is Data Management important? #7: Cornelia Wetzker

Although processing and analyzing multidimensional data sets can be quite demanding, it is important to conduct research in a #FAIR and sustainable manner. The @nfdi4bioimage@nfdi.social data stewards can help by providing training on proper data handling and annotation.

👉 If you want to learn more about data management or need help with image data annotation, feel free to contact Cornelia via https://nfdi4bioimage.de/help-desk/

Love Data Week 2026, the international week dedicated to research data and #ResearchDataManagement, started yesterday.
We would like to highlight the virtual Coffee Lecture "Open Science, Open Data & KonDATA - Publishing research data sustainably and making it accessible" by our @nfdi4bioimage@nfdi.social data steward Maximilian Müller (Team Open Science, University of Konstanz) on February 11 from 1:00 – 1:45 pm.
You can participate online via Zoom; registration is not required.
👉 https://www.kim.uni-konstanz.de/kim-news/news-detailseite/love-data-week-2026/

Dear bioimage enthusiasts!
Jointly organized by @nfdi4bioimage@nfdi.social & @eurobioimaging@bird.makeup we invite you to bring reproducible image analysis to the cloud. Have you established worksflows that make bioimage data analysis FAIR? Help others reuse your workflow by making them available for the bioimaging community in Galaxy @galaxyfreiburg@xn--baw-joa.social Come to Freiburg from February 26th to March 1st. It is a hybrid event, online participation is possible. Details and registration: https://galaxyproject.org/events/2024-02-26-hackathon-image-analysis-in-galaxy/

#opensciencefestival in Mainz. Meet Ksenia, our Data Steward in @nfdi4bioimage@nfdi.social at the #NFDI market booth.

The booth is a collaborative effort across the consortia.

See also:
https://nfdi.social/@punch4nfdi/113153175600587929
https://nfdi.social/@nfdi4plants/113152804823983285
https://nfdi.social/@nfdi4culture/113151995540315390
and others.

Looking forward to meeting you there!

In the poster "Develop an LLM-based framework for translating KNIME workflows into Galaxy Imaging workflows" K.Nguyen, M. Bernt, T. Schnicke, @haesleinhuepf@mastodon.social and R. Massei present a KNIME-to-Galaxy workflow that successfully extracts KNIME node configurations, processes them using LLM-based imaging, and generates valid Galaxy workflow structures.

Find the poster with the workflow here:
👉 https://doi.org/10.5281/zenodo.17775760
and check out the corresponding GitHub repository:
👉 https://github.com/rmassei/imaging_KNIME_to_Galaxy

We have some bad news, but also some good news, regarding the 19th Open Microscopy Environment (#OME) Community Meeting from 28.-30.4.2026!

We are pleased to announce that we have already reached the maximum capacity for registrations.Unfortunately, this means that on-site registration is no longer possible. To ensure that everyone can still participate, we have decided to hold the event in a hybrid format.

👉 Receive further information about your online participation: https://gerbi-gmb.de/machform/view.php?id=100870

You can't spell AI without FAIR❗

Here are the presentation slides from
Johannes Soltwedels
talk, "You Can't Spell AI Without FAIR: How Data Management Leaves Footprints in Image Analysis," presented at the #ELMI2026 conference.

👉 Find the presentation on Zenodo: https://doi.org/10.5281/zenodo.20708139

In March, @haesleinhuepf@mastodon.social gave a talk at the University of Copenhagen on "How Generative Artificial Intelligence Impacts BioImage Data Science".

His presentation was filmed and shared by Danish BioImaging and includes his experience and experiments with Large Language Models (LLMs) and Vision Language Models (VLMs) for bioimage analysis, as well as insights into their capabilities.

Find his slides on zenodo:
👉 https://doi.org/10.5281/zenodo.18879905

and the full video on Youtube:
👉 https://www.youtube.com/watch?v=Nw40Mbh8eLI&t=1218s

The 11th International Conference on Plasma Medicine (ICPM) is currently taking place in Gifu, Japan.
@nfdi4bioimage@nfdi.social Data Steward @mohsenahmadi@nfdi.social (INP Greifswald) joined the conference and presented his work on a "Bioimaging Data Management Workflow for Plasma Medicine" there. He and his co-authors developed a workflow that implements the FAIR principles across the entire lifecycle of bioimaging data in plasma medicine.

Read more about the workflow:
👉 https://www.biorxiv.org/content/10.64898/2026.01.26.700509v1

Save the Date: Build Skills. Show Tools. Share Data 💥

Boosting Biodata Bootcamp on Sep 15 to 17, at @rwthaachenuniversity with @FAIRagro@nfdi.social, @nfdi4plants@nfdi.social, #nfdi4biodiversity, @nfdi4bioimage@nfdi.social and @NFDI4Microbiota@nfdi.social.

We invite you to submit your abstracts starting from April 1st.
Registration for the Boosting Biodata Bootcamp 2026 will open on May 1st.

👉 events.hifis.net/event/3702/

On March 2, Yi Sun (@nfdi4bioimage@nfdi.social, @embl@bird.makeup) presented his poster "Cloud-Based Virtual Desktops for Reproducible Research" at the first Stuttgart Research Software Day which took place prior to the 6th Conference for Research Software Engineering in Germany #deRSE26 in Stuttgart.

Find more info about the different types of cloud-based virtual desktops Yi Sun and his colleagues provide here:
👉 https://zenodo.org/records/17092303

Are you unsure about the best way to import or export your data in OMERO? Which platforms, programs, and formats are actually compatible with it?

At the last #RDM4MIC meeting in the fall, @nfdi4bioimage@nfdi.social researcher Niraj Kandpal gave a presentation titled “Data Integration and Interoperability with ARC, OMERO, 3DSlicer, and OME-Zarr”, addressing those questions.

View his slides on Zenodo:
👉 https://doi.org/10.5281/zenodo.17487263

and watch the recording of his talk on YouTube:
🎬 https://www.youtube.com/watch?v=Hw8jpNxaPIk

@mohsenahmadi@nfdi.social 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 @resdatall@mastodon.social (#rdade2026). This workflow automatically links image data, metadata, and experimental documentation, thereby improving the reproducibility, comparability, and reusability of research data.

👉 View the poster on #Zenodo: https://zenodo.org/records/18454238

At the #ELMI2026 Core Facility Day, Christian Schmidt presented the #BAND (BioImage Analysis Desktop) service by @nfdi4bioimage@nfdi.social on behalf of its core developer Yi Sun from @embl@bird.makeup Heidelberg.

BAND is a user-friendly, specially developed virtual platform for advanced image analysis: low-barrier access to powerful compute resources for bioimage analysis available in the cloud.

Go to BAND: https://bandv1.denbi.uni-tuebingen.de/#/eosc-landingpage

The second @nfdi4bioimage@nfdi.social newsletter of the year has been published and covers what’s new, what’s upcoming, and what to read and review within the bioimaging community.

In addition to a carefully curated list of events in the coming months that we recommend – and where you can meet our researchers – you’ll find important information and links to news and developments within the consortium.

Here you can find the latest issue or sign up for the newsletter:
👉 https://nfdi4bioimage.de/en/news/newsletter/

📅 The May image in the @nfdi4bioimage@nfdi.social wall calendar
If you want to publish your data, it’s important to think beyond image acquisition und image analysis. Toward the end of her project, Vivien Strotmann, the author of this month’s image, reached out to the NFDI4BIOIMAGE data stewards to tackle the task of data transformation and make her data reusable.
Read more about the story behind the May image:
👉 https://nfdi4bioimage.de/en/community/wall-calendar/wall-calendar-2026/#May2026
Find the dataset on BioImage Archive:
👉 https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1636