Recently added (10)#
“Data Stewardship at NFDI4BIOIMAGE” presentation at Data Stewardship Knowledge Exchange Event @EMBL-Heidelberg#
Jens Wendt
Published 2026-05-18
Licensed CC-BY-4.0
Presentation held at the Data Stewardship Knowledge Exchange Event at EMBL-Heidelberg in May 2026 about the implementation of Data Stewardship at NFDI4BIOIMAGE. We acknowledge funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI 46/1 – 501864659.
Building Research Infrastructure Communities That Last#
Carole Goble
Published 2026-05-01
Licensed CC-BY-4.0
Invited keynote for 19th OME Community Meeting, Düsseldorf, Germany, 28-30 April 2026, https://www.openmicroscopy.org/events/ome-community-meeting-2026.html
How Generative Artificial Intelligence impacts Bio-image Data Science#
Robert Haase
Published 2026-06-02
Licensed CC-BY-4.0
In this presentation we learn about the impact of generative artificial intelligence (AI), and in particular large language models (LLMs), on the field of bio image analysis. We dive deeper into data analysis code-generation and AI systems built around LLMs integrating code generation in our workflows conveniently:
bia-bob git-bob sand-bob
Finally, we take a look at how these systems can be used on sovereign infrastructure to support privacy in a scientific context.
NFDI4BIOIMAGE Interim Progress Report (03/2023 - 02/2026)#
Josh Moore, Christian Schmidt, Robert Haase, Jan-Philipp Mallm, Carsten Fortmann-Grote, Thilo Figge, Christian Tischer, Yi Sun, Thomas Zobel, Jens Wendt, Björn Grüning, Susanne Kunis, Markus Blank-Burian, Ami Trivedi, Janina Hanne, von Suchodoletz, Dirk, Michael Scherle, Riccardo Massei, Cornelia Wetzker, Maximilian Müller, Marie Baldenius, Inga Mohr, Vanessa Fuchs, Tobias Gottschall, Michele Bortolomeazzi, Ruman Gerst, Mohsen Ahmadi, Jianxu Chen, Markus Becker, Elisa Ferrando-May, Stefanie Weidtkamp-Peters
Published 2026-06-02
Licensed CC-BY-4.0
Interim Progress Report of the Consortium NFDI4BIOIMAGEPart 1 published at: https://www.dfg.de/en/research-funding/funding-initiative/nfdi/progress-reportsPart 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.
[1] https://youtu.be/7nj2BkRJ8Q0
Sample image data and annotations associated to Presynaptic Actin Nanostructures: A Reproducibility Case Study#
Rensu Theart, Florian Levet, Hernandez-Herrera, Christophe Leterrier, de la Ballina, Laura R
Published 2026-05-26
Licensed CC-BY-4.0
Raw, processed and annotated images associated with the manuscript “Presynaptic Actin Nanostructures: A Reproducibility Case Study”. This work is part of an initiative of the Global BioImage Analysts’ Society (GloBIAS) to assess reproducibility of published bioimage analysis workflows. We present our attempt to reproduce Figure 7 of the article Presynapses contain distinct actin nanostructures. J Cell Biol 2 October 2023; 222 (10): e202208110. doi: https://doi.org/10.1083/jcb.202208110. Original images and annotations were kindly provided by their authors.
[BINA] Understanding the Standardization Runway of OME-Zarr#
Josh Moore
Published 2026-05-20
Licensed CC-BY-4.0
40 Minute talk presented to the BINA Insights and Educational Tools from Industry Series https://www.bioimagingnorthamerica.org/events/insights-and-educational-tools-from-industry-series-registration/
[FDM-Werkstatt 2026] [talk] NFDI - Nationale Forschungsdaten Infrastruktur -2 Lifescience consortia - NFDI4BIOIMAGE + DATAPlant#
Fuchs, Vanessa Aphaia Fiona
Published 2026-03-31
Licensed CC-BY-4.0
This publication contains the slides from the presentation “NFDI - Nationale Forschungsdaten Infrastruktur - 2 Lifescience consortia - NFDI4BIOIMAGE + DATAPlant” held on the 24th of March 2026 during the FDM Werkstatt 2026 in Düsseldorf.
[OME2026] Poster:Putting FAIR Principles into Action - Euro-BioImaging’s FAIR Data Toolkit#
Isabel Kemmer, Euro-BioImaging ERIC
Published 2026-04-28
Licensed CC-BY-4.0
Abstract: Euro-BioImaging Image Data Services includes the FAIR Data Toolkit to support its network of Nodes and their research communities in implementing robust bioimage data handling. This toolkit includes customizable data management plan templates, metadata & deposition guides, repository decision trees and a collection of training resources and consultation opportunities. All of these are designed to provide guidance around the entire bioimage data lifecycle, from acquisition to reuse. Beneath the surface of these resources, OME standards and tools provide the technical foundations for interoperability. Whether it’s OME metadata standards, Bio-Formats, OMERO, OME-Zarr, or the IDR, all of them are woven into the toolkit and shape our trainings and consultations. To enable broad adoption of OME-Zarr, we’re also creating open-source tools that streamline conversion and work with it. Through this OME integration, Euro-BioImaging turns FAIR community solutions into everyday practice by equipping Nodes with ready-to-use resources for their staff and researchers. Nodes adapt and distribute the toolkit locally, amplifying standardized, reproducible, and interoperable data handling across Europe’s bioimaging community. Note: this digital version of the poster was updated on 2026-05-27 with the latest numbers for Euro-BioImaging facilities and Image Data Community Days and is therefore slightly different than the one presented at the meeting.
[TiM2025] Hands-on: Creating Bio-image Overviews with OMERO.figure#
Cornelia Wetzker, Mohsen Ahmadi, Ksenia Krooß, Jens Wendt, Tom Boissonnet
Published 2026-06-09
Licensed CC-BY-4.0
The slides are part of a hands-on session that demonstrates the usage of OMERO.figure to create overviews of microscopy images and datasets presented at the Workshop Data Stewardship in Microscopy at the Trends in Microscopy 2025. Usage of the material in self learning: To be able to follow the hands-on material, find the 3 example datasets of the workshop openly accessible in a public user space of an OMERO instance at the University of Münster via this link: https://omero-tim.gerbi-gmb.de/webclient/?show=dataset-25739 Alternatively, open the tool omero.figure in this instance directly (https://omero-tim.gerbi-gmb.de/figure/) and add one of the datasets by providing its id: 105986. (see the slides for details) Origin of the microscopy dataset: The datasets originate from a project dealing with fluorescence lifetime imaging microscopy (FLIM) and its possible application to distinguish spectrally overlapping fluorophores based on their lifetimes. The scientific context and further processing of the image datasets are described in the following publication: https://doi.org/10.1111/jmi.70036 The complete bioimage dataset including experimental, microscopy and image analysis metadata can be found on the BioImage Archive: https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1967
[Workshop] Imaging data management with OMERO - Hands-on - by Vanessa Fuchs | NFDI4BIOIMAGE#
Fuchs, Vanessa Aphaia Fiona
Published 2026-04-01
Licensed CC-BY-4.0
In this workshop the participants get an introduction to OMERO and its core concepts (projects, datasets, images, metadata, permissions). Additionally they perform a few hands-on tasks: OMERO functionalities, data annotation using a REMBI table, and OMERO.figure. This workshop was part of the FDM-Werkstatt 2026 in Düsseldorf.
https://zenodo.org/records/19366801
https://doi.org/10.5281/zenodo.19366801