NFDI4BIOIMAGE Interim Progress Report (03/2023 - 02/2026)

Interim Progress Report of the Consortium NFDI4BIOIMAGE
Part 1 published at: https://www.dfg.de/en/research-funding/funding-initiative/nfdi/progress-reports
Part 2 published here.

Biological imaging is a core pillar of modern life science, enabling quantitative insight across scales and disciplines, from molecular biology to medicine. Increasingly, imaging is combined with other data modalities such as genomics and proteomics, positioning bioimaging at the heart of phenomics and integrative research. At the same time, bioimaging experiments are among the largest and most heterogeneous produced in academia, often surpassing terabyte scale. Without shared standards, scalable infrastructure, and coordinated community practices, much of this data risks remaining siloed or non-reusable, limiting its scientific value for the wider research community. NFDI4BIOIMAGE was established to address these challenges by embedding the German bioimaging community within a strong international ecosystem and contributing to long-standing global goals around data acquisition, management, discovery, and publication. Three years into its five-year funding period, NFDI4BIOIMAGE has become a visible and trusted actor in shaping how bioimaging data are standardized, shared, analyzed, and sustained, both nationally and internationally^[1]. At its inception, the consortium defined four closely linked objectives, spanning the full bioimaging data lifecycle and aligning national efforts with international developments (Figure 1).

A central objective of NFDI4BIOIMAGE has been to champion open, community-driven standards (Obj. 1) that enable data to be reused across tools, institutions, and scientific domains. The consortium has led the development and international adoption of a Next-Generation File Format (NGFF) through a Request for Comments (RFC) process. This work directly addresses the needs of modern, cloud-scale, and multimodal imaging and has attracted sustained engagement from global partners, including follow-on funding from international sources such as Wellcome and Biohub. NGFF, however, goes beyond a file format, by enabling systematic extension in other ecosystems, like the emerging SpatialData standard for the specific needs of spatially resolved omics. This serves as a blueprint for domain-specific specialization from a shared core standard. In collaboration with the BioImage Archive (BIA) at EBI, the consortium is contributing to interoperable metadata specifications that move bioimaging closer to FAIR Digital Objects (FDOs), or “FAIR Image Objects” (FAIR-IO). Additional contributions include promotion of REMBI (Recommended Metadata for Biological Images) as a de facto metadata standard, RO-Crate–based packaging approaches, and expanding our data ambassador model into FAIR data champions who drive community adoption.

To make standards usable in practice, NFDI4BIOIMAGE has invested heavily in scalable, interoperable infrastructure (Obj. 2) supporting both national and international workflows. This includes cloud-ready analysis environments based on Jupyter, object storage, Desktop-as-a-Service (DaaS) and workflow platforms such as Galaxy, enabling reproducible analysis of large imaging datasets across infrastructures. The consortium has supported the migration of major international resources, including the Image Data Resource (IDR), to scalable cloud-based access models and has worked closely with EMBL-EBI to convert BioImage Archive holdings into REMBI-annotated NGFFs, namely OME-Zarr, substantially improving online accessibility and reuse.

At the software level, NFDI4BIOIMAGE has strengthened tools for maximizing reproducible bioimage analysis (Obj. 3), such as Galaxy and JIPipe, adding features including RO-Crate packaging, OME-Zarr support, and OMERO integration to bridge experimental analysis pipelines with FAIR data publication. The BioImage ANalysis Desktop (BAND) has served as a key transitional DaaS platform, bringing users’ experience closer to their large-scale imaging data in the cloud while maintaining an interactive, reproducible computational environment, which is particularly effective for training and lowering barriers to advanced analysis. The consortium has also engaged with emerging AI ecosystems like Hugging Face, aligning bioimaging workflows with broader developments in machine learning and reproducible research. In parallel, the consortium has supported local data stewardship and storage solutions at multiple German institutions and the operation of federated OMERO services, ensuring national capacity grows in step with international alignment.

A defining strength of NFDI4BIOIMAGE is its emphasis on capacitating researchers through training and data stewardship (Obj. 4). Over the past three years, the consortium has delivered a broad program of training and capacity building, including institutional workshops, national courses, and contributing to major international conferences, and enhanced access to open educational resources for bioimaging RDM. Flagship initiatives such as RDM4mic and I3D:bio have significantly raised awareness and competence around research data management in bioimaging by giving the community a platform to actively engage. NFDI4BIOIMAGE has, furthermore, helped professionalize data stewardship roles through helpdesks and cross-consortia collaboration, supported data submission to the BioImage Archive, and improved discoverability through catalogs of tools, services, and use cases integrated into institutional research structures.

In addition, NFDI4BIOIMAGE contributes actively beyond its consortium. The speaker has chaired the NFDI Konsortialversammlung while members participate broadly in relevant NFDI Sections, notably those focused on metadata (including ontologies, search, and knowledge graphs) and on common infrastructure and data integration. Internationally, consortium members contribute to ISO standardization, provide leadership within the Open Microscopy Environment (OME), and represent bioimaging interests in the European Open Science Cloud (EOSC). Engagement in initiatives such as IO-FAST and foundingGIDE, together with close ties to Global BioImaging, further amplify Germany’s visibility in the global imaging landscape. For the final two years of funding, NFDI4BIOIMAGE’s priorities include the formal standardization of widely adopted practices for bioimage data, establishment of a national OMERO framework in coordination with de.NBI (underpinned by an MoU), and the development of sustainable operational models for bioimaging data services. While challenges remain, particularly around long-term sustainability and scaling, the consortium has laid a robust foundation. By combining standards, infrastructure, tools, and people, NFDI4BIOIMAGE has positioned Germany as a central contributor to a FAIR, reproducible, globally connected bioimaging ecosystem.