Our work program
Our consortium works towards four main goals: advancing standards for bioimage data, providing scalable infrastructure for FAIR bioimage data, supporting reproducible image analysis workflows, and empowering researchers in FAIR bioimage data management.
To fulfill these goals, our work program is organized in six Task Areas. As the NFDI4BIOIMAGE consortium is a bottom-up project from the communtiy for the community, close collaboration of our members and participating institutions is inevitable. All our activities are dedicated to improving the capabilities and the capacity for bioimaging research data management in the scientific community. Find our partners here.
Task Areas
We are organised into six Task Areas. Four Task Areas focus on developing and improving technical solutions for bioimage data management. Two Task Areas address coordination and governance, with a strong emphasis on community engagement, training, and support for researchers.
Each Task Area is led by two or three experts from our partner institutions. The full work programme is described in the NFDI4BIOIMAGE proposal, which is available on Zenodo.
Task Area 1: Image (meta)data, Formats and Standardization
Key words: OME.zarr – NGFF – FAIR-IO (an FDO concept) – JSON-LD – RDF – OME.OWL
In Task Area 1, the harmonisation and further development of image data formats and metadata standards is a key focus. Standardised formats are essential to ensure interoperability across different data types and data management systems. This requires annotations that are both machine-actionable and easy for humans to understand.
An important recent international effort within the bioimaging community is the development of next-generation file formats (NGFF) for imaging data, to which we actively contribute. NGFFs are promising candidates for globally harmonised image formats and, among other advantages, support cloud-based handling of large-scale image data. As a result, this topic has strong potential to become a cross-cutting activity within the NFDI.
The current next-generation file format for bioimaging data is OME-Zarr. OME-Zarr enables efficient, random access to multi-dimensional image data, allowing users to access individual planes or views without loading entire datasets. It also supports streaming of image data over the Internet, so that only the required data are transferred. The ecosystem of tools for OME-Zarr-based visualisation and image analysis is growing steadily. OME-Zarr is a central pillar of the NFDI4BIOIMAGE FAIR-IO concept (FAIR Image Objects). FAIR-IO implements the principles of FAIR Digital Objects (FDO) for bioimaging by combining image data with associated digital assets, rich metadata, and unique identifiers. This structure enables linked data approaches and ensures long-term machine-readability and reuse.
Selected publications
- Moore, Josh, Kunis, Susanne. Zarr – A Cloud-Optimized Storage for Interactive Access of Large Arrays, Vol. 1 (2023): 1st Conference on Research Data Infrastructure (CoRDI) – Connecting Communities. Link to source. Find conference proceedings here. Scholarly work can be found here.
- Moore, Josh; Waagmeester, Andra; Hettne, Kristina; Wolstencroft, Katherine; Kunis, Susanne (2024): „RDF as a bridge to domain-platforms like OMERO, or There and back again.“ Link to source.
- Moore, Josh; Kunis, Susanne (2024): „AI’s Dirty Little Secret: Without FAIR Data, It’s Just Fancy Math“. Link to source.
- Moore, J., Basurto-Lozada, D., Besson, S. et al. OME-Zarr: a cloud-optimized bioimaging file format with international community support. Link to source.
- Moore, Joshua Allen. (2023). Zarr: A Cloud-Optimized Storage for Interactive Access of Large Arrays. 1st Conference on Research Data Infrastructure (CoRDI), Karlsruhe, Germany. Link to source. Find the conference poster here. Scholarly work can be found here.
- Brooks, Michael. (2023). How open-source software could finally get the world’s microscopes speaking the same language. Link to source.
- Moore J, Allan C, Besson S, et al (2021) OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies. Link to source.
- Moore, J. A., & Kunis, S. (2023). NFDI4BIOIMAGE: Perspective for a national bioimage standard. Link to source. Find the conference poster here. Scholarly work can be found here.
- Moore, J., Kunis, S., Grüning, B., Blank-Burian, M., Mallm, J.-P., Stöter, T., Zuschratter, W., Figge, M. T., Kreshuk, A., Tischer, C., Haase, R., Zobel, T., Bauer, P., Svensson, C.-M., Gerst, R., Hanne, J., Schmidt, C., Becker, M. M., Bocklitz, T., … Weidtkamp-Peters, S. (2024). NFDI4BIOIMAGE – National Research Data Infrastructure for Microscopy and Bioimage Analysis. Link to source.
Task Area 2: Technical Infrastructure and Cloud Resources
Key words: Infrastructure as a Service (IaaS) – Desktop as a Service (DaaS) – Training – Infrastructure as a Service (TIaaS) – Jupyter – Pulsar – Galaxy – OMERO
Task Area 2 provides technical infrastructure and cloud resources and serves as a central enabler for the consortium and the community, including “sandbox” environments for testing of new tools and services. They also provide access to image analysis workflows that require high computational resources in collaboration with TA4.
Task Area 3: Multimodal data linking and integration
Key words: Interoperability – Multimodal graph database – Spatial omics technologies – Sample (metadata) tracking
Task Area 3 focuses on linking bioimage data with other data types and connecting image-specific data management systems to more general research data infrastructures. It also includes targeted collaborations with other consortia to develop and align shared data structures.
Task Area 4: Bioimage Informatics and Analysis
Key words: Reproducible analysis workflows – JiPipe – Fiji/ImageJ – Bioimage analysis desktop (BAND) – Galaxy – Jupyter Notebooks
Task Area 4 promotes reproducible bioimage analysis workflows by improving interoperability between widely used tools. In close collaboration with Task Area 2, they also work to make state-of-the-art analysis methods accessible to the entire bioimaging community. Together with Task Area 5, Task Area 4 contributes to training materials that support the effective use of new and advanced analysis approaches.
Task Area 5: Training and Community Integration
Task Area 6: Coordination, Governance, and Networking
Key words: National and international networking – Administration and organization – Evaluation and reporting – Strategy and monitoring – Outreach and public representation – Coordination of the work in Sections and cross-cutting topics in the NFDI association
Task Area 6 oversees the overall coordination and management of the project. It is responsible for executive project management, as well as outreach and networking activities that connect the consortium with the wider research community. Task Area 6 also hosts the NFDI4BIOIMAGE Coordination Office, which serves as the central hub for communication, organisation, and support across all Task Areas.
Our members
All members, who are co-applicants, share the main responsibilities for the work programme by leading one or more task areas in the work programme. The scientists leading a Task Area have the role as co-spokespersons of the consortium and responsibly represent their institutional contribution within NFDI4BIOIMAGE. Co-Applicant institutions receive funding from the consortium’s budget.
The Heinrich-Heine University Düsseldorf (HHU) is the main institution responsible for the NFDI4BIOIMAGE project at large. The consortium’s budget is administrated at HHU and transferred to other member institutions based on a Fund Transfer and Collaboration Agreement. The HHU’s responsible scientist for the consortium, Prof. Stefanie Weidtkamp-Peters, Head of the Center for Advanced Imaging (CAi) at HHU, acts as the Spokesperson of NFDI4BIOIMAGE.
Heinrich Heine University Düsseldorf (HHU)
Responsible:
Prof. Dr. Stefanie Weidtkamp-Peters
Head of the Center for Advanced Imaging (CAi)
Spokesperson of NFDI4BIOIMAGE
German Cancer Research Center (DKFZ),
Heidelberg
Responsible:
Prof. Dr. Elisa May, Chief Enabling Technology Officer (CETO)
Dr. Jan-Philipp Mallm, Head of the Single-cell Open Lab
European Molecular Biology Laboratory (EMBL),
Heidelberg
Responsible:
Dr. Anna Kreshuk, Research Unit Cell Biology and Biophysics, Machine Learning for Bioimage Analysis
Dr. Christian Tischer, Team Lead BioImage Analysis
University Münster
Responsible:
Dr. Thomas Zobel, Head of the Münster Imaging Network
Dr. Markus Blank-Burian, Univerty Münster IT
University of Osnabrück (UOS)
Responsible:
Dr. Susanne Kunis, Integrated Bioimaging (iBiOs) at Center of Cellular Nanoanalytics (CellNanOs)
Leibniz Institute for Natural Product Research and Infection Biology,
Hans Knöll Institute (HKI), Jena
Responsible:
Prof. Dr. Marc Thilo Figge, Applied Systems Biology
Cluster of Excellence Balance of the Microverse
Leibniz Institute for Neurobiology (LIN),
Magdeburg
Responsible:
Prof. Dr. Stefan Remy, Scientific Managing Director
German BioImaging – Gesellschaft für Mikroskopie und Bildanalyse e.V. (GerBI-GMB)
Responsible:
Prof. Dr. Stefanie Weidtkamp-Peters, Head of Board
Josh Moore, Senior Research Data Management Officer
University of Konstanz (UKON)
Responsible:
Prof. Dr. Elisa May, Professor for Cellular Bioimaging
Chief Enabling Technology Officer at the DKFZ
University of Leipzig (UL)
Responsible:
Dr. Robert Haase, Training Coordinator at the Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI)
University of Freiburg (ALU-FR)
Responsible:
Dr. Björn Grüning, Head of Freiburg Galaxy Team
Participating institutions
Many partners contribute regularly to the work in our Task Areas without being formally responsible for leading them. Each participating institution is represented by a project leader who coordinates its contribution to NFDI4BIOIMAGE. Participating institutions may receive funding from the consortium’s budget.
In addition to consortium members, we collaborate with consortium partners. These include international initiatives and projects, such as Euro-BioImaging ERIC or the BioImage Archive at EMBL-EBI, as well as Community Use Cases (CUCs). CUCs are stakeholders from the bioimaging community who test consortium tools and services in practice and provide feedback to improve them. All collaborations are based on mutual benefit. Consortium partners do not receive direct funding but may be supported through allocated person-hours to help achieve shared goals.
Forschungszentrum Jülich
Responsible:
Prof. Dr. Timo Dickscheid
Working Group Leader „Big Data Analytics“
Georg-August-University of Göttingen
Responsible:
Prof. Dr. Jan Huisken
Head of the Multiscale Biology lab
HAWK University of Applied Sciences and Art Hildesheim/Holzminden/Göttingen
Responsible:
Prof. Dr. Claire Chalopin
Faculty of Engineering and Health
Heidelberg University
Responsible:
Prof. Dr. Jan Lohmann
Centre for Organismal Studies (COS) Heidelberg
Helmholtz-Center for Environmental Research – UFZ,
Leipzig
Responsible:
Dr. Jan Bumberger
Head of Research Data Management & Environmental Sensor and Information Systems
Johannes Gutenberg-University Mainz
Responsible:
Prof. Dr. Paul Czodrowski
Physical Chemistry with a focus on Experimental Biophysical Chemistry
Leibniz Institute for Analytical Sciences – ISAS,
Dortmund
Responsible:
Dr. Jianxu Chen
Group Leader AMBIOM – Analysis of Microscopic BIOMedical Images
Leibniz Institute for Plasma Science and Technology – INP,
Greifswald
Responsible:
Dr. Markus Becker
Head of depertment Plasma Modelling and Data Science
Leibniz Institute of Photonic Technology – IPHT,
Jena
Responsible:
Prof. Dr. Thomas Bocklitz
Head of research department „Photonic Data Science“
Max Planck Institute for Evolutionary Biology – MPIEB,
Plön
Responsible:
Dr. Carsten Fortmann-Grote
Heaf of Scientific Computing Services Unit
Technical University of Dresden
Responsible:
Prof. Dr. Michael Schlierf
Head of B CUBE – Center for Molecular Bioengineering
University of Cologne
Responsible:
Dr. Astrid Schauss
Head of Imaging Facility CECAD
Participating persons
Dr. Jean-Marie Burel
Open Microscopy Environment Consortium, University of Dundee, UK
Our partners
The activities of NFDI4BIOIMAGE’s member institutes are integrated into the international bioimaging community through exchange and collaboration with organizations, and projects worldwide. We seek for international collaboration with interested communtiy stakeholders.
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