Image Data Community Days 2026

Discover the range of image data services offered by Euro-BioImaging Nodes, supporting users with image analysis, management, visualization, and beyond. Hear how these services have advanced research and enabled new scientific insights.

This session explores the research data lifecycle through the lens of FAIR principles, featuring showcases and best practices from Euro-BioImaging Nodes and partners to guide effective data planning, processing, sharing, and reuse.

This session explores how community‑driven Next‑Generation File Formats (NGFF) and evolving metadata standards are improving the way bioimaging data is shared, accessed, and reused. Building on these advances, the foundingGIDE project illustrates how coordinated infrastructure efforts can apply these developments to create more interoperable and sustainable bioimaging research environments.

This session introduces data management, quality control, and image processing tools for biomedical imaging developed by Euro-BioImaging Nodes and the wider scientific community. Designed for both preclinical and medical imaging scientists, these tools aim to improve workflow efficiency and analysis accuracy. Participants will learn how these solutions can streamline imaging data processing and support more reliable research outcomes.

This session explores image data management and applications across diverse research domains, featuring talks on the OSCARS FIESTA project’s data workflows in Galaxy, the Bioimage Model Zoo, and key EOSC developments to enhance cross-domain interoperability, accessibility, and innovative use cases.

Host: Aastha Mathur (Euro-BioImaging)

Description: This session features flash talks showcasing innovative image analysis and data management tools. Discover new solutions, hear from experts, and foster collaboration within the imaging community.

Target Audience: anyone interested in image data tools

Prerequisites: none

Capacity: unlimited

Host: Michele Bortolomeazzin & Christian Schmidt (German Cancer Research Center (DKFZ))

Description: OMERO has been established as a valuable, community-tested platform to facilitate research data management with bioimaging data. It allows the central, secure storage of original image files, collaborative access and analysis, metadata curation, and figure creation directly from the original data. However, deploying OMERO as a solution for laboratories, departments, or whole institutes requires a coordinated multi-stakeholder process. Consequently, researchers who would like to use OMERO as their RDM solution may be overwhelmed by the effort that an OMERO implementation demands. On the basis of the „Information Infrastructure for BioImage Data“ (I3D:bio) project, and the NFDI4BIOIMAGE consortium, we have developed structured processes and installation management approaches to realize institutional OMERO instances as a resource for all researchers. In this workshop, we share hands-on experience for the initiation and steering the OMERO implementation process. This workshop is directed primarily at research support facility staff and leaders, senior researchers, and project managers in the field of bioimaging-data-driven research fields.

Target Audience: Researchers, research support staff, IT staff, core facility staff, data stewards

Prerequisites: none, but some prior knowledge with OMERO is an asset

Capacity: unlimited

Host: Marie Held (University of Liverpool)

Description: Reproducibility is essential for credible science, yet microscopy data are especially prone to irreproducibility. This workshop will show how to make your microscopy research more reliable and FAIR (Findable, Accessible, Interoperable, Reusable). Learn practical strategies for planning, data organisation, documentation, and preparation for reuse to ensure your results stand the test of time.

Target Audience: mainly students, post-docs, PIs

Prerequisites: none

Capacity: 20

Host: Isabel Kemmer (Euro-BioImaging), Melina Velasquez (EMBL-EBI)

Description: This hands-on workshop covers depositing bioimage data into trusted repositories, starting with repository selection. It then provides a step-by-step guide to submitting data to the BioImage Archive, focusing on common challenges like data organization and metadata. The core session features hands-on practice with a mock deposition on an example dataset. Those bringing their own data can choose to participate in the optional 'Data Clinic' for personalized advice and troubleshooting.

Target Audience: researchers, data stewards, facility staff, and anyone that's curious about how to deposit data in BioImage Archive

Prerequisites: None, but participants may already familiarize themselves with the BioImage Archive and REMBI beforehand. Please feel free to bring your own dataset for deposition as well.

Capacity: 20

Host: Allison Truhlar & Konrad Rokicki (HHMI Janelia Research Campus)

Description: Fileglancer is a new web-based tool designed to simplify working with OME-Zarr image datasets. In this workshop, we will introduce Fileglancer, demonstrate its key features, and explain how it supports OME-Zarr workflows. Participants will have the opportunity to install the tool, explore their own local data, and ask questions about using it in their workflows.

Target Audience: Users of OME-Zarr and N5 data formats

Prerequisites: Working knowledge of OME-Zarr

Capacity: unlimited

Description: Working with image data can be fascinating, but it can also feel a bit isolating at times. Whether you spend your days refining algorithms, managing or curating datasets, interpreting results, or are just beginning your journey in the field, we invite you to join us in the image.sc Gather instance for a relaxed networking session for image data professionals of all backgrounds. This is an opportunity to connect with peers, exchange experiences, and share insights about careers, collaboration, and the broader world of image data. No demos or analysis required; just bring your curiosity, an open mind, and perhaps a virtual beverage of choice.

Target Audience: all interested in informal discussions and networking

Prerequisites: None

Capacity: unlimited

Host: Bugra Özdemir (Euro-BioImaging)

Description: This workshop introduces OME‑Zarr, a cloud‑native, next‑generation file format that enables efficient access to large bioimaging datasets. The session will demonstrate how essential tasks such as batch conversion, simple visualization, validation, and metadata curation can be performed using EuBI‑Bridge, a framework designed to streamline these steps within a single workflow. Participants will also be introduced to several widely used tools from the broader OME‑Zarr ecosystem for visualization, validation, and more advanced data exploration.

Target Audience: The workshop is introductory and mainly designed for bioimaging researchers with little (or no) OME-Zarr experience. However, OME-Zarr experts may also join to learn more about the EuBI-Bridge tool and contribute to the discussion.

Prerequisites: Users are not required to install any software since the workshop will be given on the Bioimage Analysis Desktop (BAND). Participants are however invited to log in to BAND with their Google accounts. This user guide for BAND is also helpful to read in advance. Participants can already learn a little bit about OME-Zarr and the ecosystem around it. For a deeper understanding, this digital book may be a good reference:

Capacity: 20

Host: Alexandra Zakieva (EMBL)

Description: Overwhelmed or excited by metadata, confused or passionate about REMBI? Experienced in managing imaging metadata or just a novice, join this gamified REMBI discovery and brainstorming session to make ALL imaging metadata FAIR. At participants request, preparing submission drafts of their data to BioImage Archive is possible.

Target Audience: Anyone working or planning to work with imaging data

Prerequisites: None (the less general preparation, the better to enjoy the game surprises). For those, who want to prepare their data for submission to BioImage Archive, prepare the data size and informal project description.

Capacity: unlimited

Host: Feriel Ramdhane (Euro-BioImaging Med-Hub) & Francesco Gammaraccio (Institute of Biostructures and Bioimaging (IBB) - National Research Council of Italy (CNR))

Description: This workshop provides instruction on how to use XNAT-PIC and QC Tools within the XNAT platform. Participants will learn how to create projects, upload imaging data, and run image quality control tools. The session will include hands-on exercises to help users become familiar with the XNAT-PIC and XNAT platform’s main functionalities.

Target Audience: Researchers and technical staff working with preclinical imaging data, including people involved in image acquisition, image processing, and image data management in animal studies.

Prerequisites: The XNAT-PIC software should be installed on your local PC, but this step can be done also at the beginning of the workshop. A user account for the XNAT instance used during the workshop will be provided to all the participants.

Reading suggestions:
1) Marcus DS, Olsen TR, Ramaratnam M, Buckner RL. The Extensible Neuroimaging Archive Toolkit: an informatics platform for managing, exploring, and sharing neuroimaging data. Neuroinformatics. 2007 Spring;5(1):11-34. PMID: 17426351. https://doi.org/10.1385/NI:5:1:11
2) Zullino, S., Paglialonga, A., Dastrù, W. et al. XNAT-PIC: Extending XNAT to Preclinical Imaging Centers. J Digit Imaging 35, 860–875 (2022). PMID: 35304674. https://doi.org/10.1007/s10278-022-00612-z

Capacity: 20

Host: Jean-Marie Burel (University of Dundee), Teresa Coarasa (EMBL-EBI)

Description: Analyse OME-Zarr images hosted publicly using models from the BioImage Model Zoo

Target Audience: Participants with basic Python programming skills

Prerequisites: Python

Capacity: unlimited

Host: Leonid Kostrykin (Heidelberg University), Vladimir Ulman (CEITEC), Beatriz Serrano-Solano (Euro-BioImaging)

Description: We introduce Galaxy as a web-based platform for FAIR image data analysis workflows. The workshop includes a brief introductory lecture path and a large hands-on section.

Target Audience: People in the life sciences and beyond interested in image data analysis, with a focus on FAIR'ness and/or HPC utilization.

Prerequisites: An up-to-date web browser (preferably Firefox).

Capacity: unlimited

Host: Johanna Bischof (Euro-BioImaging)

Description: The Virtual Pub is a weekly virtual meeting for the imaging community, where Euro-BioImaging Node experts, users, technology developers and partners discuss imaging techniques in practice and explore new and emerging technologies. More details are coming soon.
The Tech Exchange is a webinar for companies in the imaging sector to showcase their latest developments. Our Industry Board member Telight will share some exciting news!

Target Audience: all imaging enthusiasts

Prerequisites: none

Capacity: unlimited