Publications
Publications that present research developed within the consortium, reflecting our joint scientific work and methodological advances.
2025
MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis
Zulueta-Coarasa, T., Jug, F., Mathur, A. et al. Nat Methods (2025).
DOI: https://doi.org/10.1038/s41592-025-02835-8.
High-content screening (HCS) workflows for FAIR image data management with OMERO
Massei, R., Busch, W., Serrano-Solano, B. et al. Sci Rep 15, 16236 (2025).
DOI: https://doi.org/10.1038/s41598-025-00720-0
Towards transparency and knowledge exchange in AI-assisted data analysis code generation
Haase, R. Nat Comput Sci 5, 271–272 (2025).
DOI: https://doi.org/10.1038/s43588-025-00781-1
2024
Progress on the interoperability between ARC (annotated research context) and the image data management system OMERO
ARC is an ISA-based metadata standard developed in the plant sciences community by the consortium DataPLANT. For image data, we work collaboratively on the interoperability between ARC and the well-established image data management system OME Remote Objects (OMERO). To this end, two hackathons took place in November, and December 2023, resulting in a first extended documentation on advancing OMERO and ARC interoperability. Find these interim results published on Zenodo: https://doi.org/10.5281/zenodo.10617006
Making the most of bioimaging data through interdisciplinary interactions
Uhlmann, V., Hartley, M., Moore, J., Weisbart, E., Zaritsky, A. (2024).
DOI: https://doi.org/10.1242/jcs.262139
Setting up an institutional OMERO environment for bioimage data: Perspectives from both facility staff and users
Jannasch, A., Tulok, S., Okafornta, C.W., Kugel, T., Bortolomeazzi, M., Boissonnet, T., Schmidt, C., Vogelsang, A., Dittfeld, C., Tugtekin, S.-M., Matschke, K., Paliulis, L., Thomas, C., Lindemann, D., Fabig, G., & Müller-Reichert, T. (2024). Journal of Microscopy, 1–15.
DOI: https://doi.org/10.1111/jmi.13360
NFDI4BIOIMAGE - National Research Data Infrastructure for Microscopy and Bioimage Analysis
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). Zenodo.
DOI: https://doi.org/10.5281/zenodo.13168693
Towards Preservation of Life Science Data with NFDI4BIOIMAGE
Haase, Robert (2024). Zenodo.
DOI: https://zenodo.org/doi/10.5281/zenodo.13506640
Photonic data analysis in 2050
Ryabchykov, Oleg; Guo, Shuxia; Bocklitz, Thomas (2024). Vibrational Spectroscopy.
DOI: https://doi.org/10.1016/j.vibspec.2024.103685
Who you gonna call? – Data Stewards to the rescue
Fuchs, Vanessa Aphaia Fiona; Wendt, Jens; Müller, Maximilian; Ahmadi, Mohsen; Massei, Riccardo; Wetzker, Cornelia (2024). Zenodo.
DOI: https://zenodo.org/doi/10.5281/zenodo.10730423
[ELMI 2024] AI's Dirty Little Secret: Without FAIR Data, It's Just Fancy Math
Moore, Josh; Kunis, Susanne (2024). Zenodo.
DOI: https://zenodo.org/doi/10.5281/zenodo.11235512
RDF as a bridge to domain-platforms like OMERO, or There and back again
Moore, Josh; Waagmeester, Andra; Hettne, Kristina; Wolstencroft, Katherine; Kunis, Susanne (2024). Zenodo.
DOI: https://zenodo.org/doi/10.5281/zenodo.10687658
[Community Meeting 2024] Supporting and financing RDM projects within GerBI
Weidtkamp-Peters, Stefanie; Moore, Josh; Schmidt, Christian; Nitschke, Roland; Kunis, Susanne; Zobel, Thomas (2024). Zenodo.
DOI: https://zenodo.org/doi/10.5281/zenodo.10889693
The role of Helmholtz Centers in NFDI4BIOIMAGE - A national consortium enhancing FAIR data management for microscopy and bioimage analysis
Massei, Riccardo; Schmidt, Christian; Bortolomeazzi, Michele; Thoennissen, Julia; Bumberger, Jan; Dickscheid, Timo; Mallm, Jan-Philipp; Ferrando-May, Elisa (2024). Zenodo.
DOI: https://zenodo.org/doi/10.5281/zenodo.11501661
SpatialData: an open and universal data framework for spatial omics
Marconato L, Palla G, Yamauchi KA, Virshup I, Heidari E, Treis T, Vierdag WM, Toth M, Stockhaus S, Shrestha RB, Rombaut B, Pollaris L, Lehner L, Vöhringer H, Kats I, Saeys Y, Saka SK, Huber W, Gerstung M, Moore J, Theis FJ, Stegle O. (2024). Nature Methods.
DOI: https://doi.org/10.1038/s41592-024-02212-x
From Paper to Pixels: Navigation through your Research Data - presentations of speakers
Zoccoler, Marcelo; Bekemeier, Simon; Boissonnet, Tom; Parker, Simon; Bertinetti, Luca; Gentzel, Marc; Massei, Riccardo; Wetzker, Cornelia (2024). Zenodo.
DOI: https://zenodo.org/doi/10.5281/zenodo.11548616
Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data
Nikki Bialy, Frank Alber, Brenda Andrews, Michael Angelo, Brian Beliveau, Lacramioara Bintu, Alistair Boettiger, Ulrike Boehm, Claire M. Brown, Mahmoud Bukar Maina, James J. Chambers, Beth Cimini, Kevin Eliceiri, Rachel Errington, Orestis Faklaris, Nathalie Gaudreault, Ronald N. Germain, Wojtek Goscinski, David Grunwald, Michael Halter, Dorit Hanein, John W. Hickey, Judith Lacoste, Alex Laude, Emma Lundberg, Jian Ma, Leonel Malacrida, Josh Moore, Glyn Nelson, Elizabeth Kathleen Neumann, Roland Nitschke, Shichi Onami, Jaime A. Pimentel, Anne L. Plant, Andrea J. Radtke, Bikash Sabata, Denis Schapiro, Johannes Schöneberg, Jeffrey M. Spraggins, Damir Sudar, Wouter-Michiel Adrien Maria Vierdag, Niels Volkmann, Carolina Wählby, Siyuan (Steven)Wang, Ziv Yaniv, Caterina Strambio-De-Castillia (2024). arXiv:2401.13022.
DOI: https://doi.org/10.48550/arXiv.2401.13022
The global RNA–RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division
Ruhland E, M. Siemers, R. Gerst, F. Späth, L.N. Vogt, M.T. Figge, K. Papenfort, & K.S. Fröhlich (2024). Proc. Natl. Acad. Sci. U.S.A. 121 (9) e2317322121.
DOI: https://doi.org/10.1073/pnas.2317322121
2023
Metadata Annotation Workflow for OMERO with Tabbles
Wendt Jens. (2023, September 4). Zenodo.
DOI: https://doi.org/10.5281/zenodo.8314968
Thinking data management on different scales
Kunis, Susanne. (2023, August 31). PoL BioImage Analysis Symposium Dresden 2023, Zenodo.
DOI: https://doi.org/10.5281/zenodo.8329306
Zarr: A Cloud-Optimized Storage for Interactive Access of Large Arrays, Vol. 1
Moore, Josh, Kunis, Susanne (2023). 1st Conference on Research Data Infrastructure (CoRDI) – Connecting Communities.
DOI: https://doi.org/10.52825/cordi.v1i.285
Zarr: A Cloud-Optimized Storage for Interactive Access of Large Arrays
Moore, Joshua Allen. (2023). [CORDI 2023] 1st Conference on Research Data Infrastructure (CoRDI), Karlsruhe, Germany. Zenodo.
DOI: https://doi.org/10.5281/zenodo.8340248
Conference talk: The Pelagic Imaging Consortium meets Helmholtz Imaging, 5.10.2023, Hamburg
Massei, Riccardo. (2023, October 6). Zenodo.
DOI: https://doi.org/10.5281/zenodo.8414319
Combining the BIDS and ARC Directory Structures for Multimodal Research Data Organization
Stöter, Torsten, Gottschall, Tobias, Schrader, Andrea, Zentis, Peter, Valencia-Schneider, Monica, Kandpal, Niraj, Zuschratter, Werner, Schauss, Astrid, Dickscheid, Timo, Mühlhaus, Timo, & von Suchodoletz, Dirk. (2023). 1st Conference on Research Data Infrastructure (CoRDI 2023), Karlsruhe, Germany. Zenodo.
DOI: https://doi.org/10.5281/zenodo.8349563
[SWAT4HCLS 2023] NFDI4BIOIMAGE: Perspective for a national bioimage standard (Version v4)
Moore, J. A., & Kunis, S. (2023). Zenodo.
DOI: https://doi.org/10.5281/zenodo.7928333
2022
Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey
Schmidt C, Hanne J, Moore J et al. [version 2; peer review: 2 approved]. F1000Research 2022, 11:638
DOI: https://doi.org/10.12688/f1000research.121714.2
2021
NFDI4BIOIMAGE - An Initiative for a National Research Data Infrastructure for Microscopy Data
Schmidt, C. and E. Ferrando-May, in E-Science Tage – Share your Research Data. 2021: Heidelberg.
DOI: 10.11588/heidok.00029489
NFDI4BIOIMAGE – An Initiative for a National Research Data Infrastructure for Microscopy Data
Schmidt, Christian und Ferrando-May, Elisa; in Heuveline, Vincent und Bisheh, Nina (Hrsg.): E-Science-Tage 2021: Share Your Research Data, Heidelberg: heiBOOKS, 2022, S. 339–343.
DOI: https://doi.org/10.11588/heibooks.979.c13747
Publications by external researchers that were enabled or strengthened through the consortium’s support, for example via collaborations initiated through the Help Desk.
In vivo application of a glutaraldehyde-free, UVA/riboflavin cross-linked bovine pericardium confirms suitability for cardiovascular substitutes
Anett Jannasch, Cindy Welzel, Jessica Pablik, Elizabeth von Hauff, Roberta Galli, Jan Rix, Antje Schauer, Claudia Dittfeld, Sems-Malte Tugtekin (2024). https://doi.org/10.1063/5.0182672
(OMERO instance of Dresden Technical University)
Analysis of vascular disruption in zebrafish embryos as an endpoint to predict developmental toxicity - High Content Screening Raw Data (OBI/WIK strain)
Julia Nöth, Stefan Scholz, Wibke Busch, Tamara Tal, Chih Lai, Akhil Ambekar, Riccardo Massei (2023). BioStudies, S-BIAD954. https://www.ebi.ac.uk/biostudies/BioImages/studies/S-BIAD954 (BioImage Archive)
Highlighting the hidden: A tagging strategy for monitoring the association of GABARAP with microtubules in living cells
Metadata Annotation Workflow for OMERO with Tabbles
Alina Üffing, Lisa Gold, Thomas Gensch, Oliver H. Weiergräber, Silke Hoffmann, Dieter Willbold (2023). BioStudies, S-BIAD952. https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD952
(BioImage Archive)