The Information Infrastructure for BioImage Data (I3D:bio) project to advance FAIR microscopy data management for the community
Creators
Description
Research data management (RDM) in microscopy and image analysis is a challenging task. Large files in proprietary formats, complex N-dimensional array structures, and various metadata models and formats can make image data handling inconvenient and difficult. For data organization, annotation, and sharing, researchers need solutions that fit everyday practice and comply with the FAIR (Findable, Accessible, Interoperable, Reusable) principles. International community-based efforts have begun creating open data models (OME), an open file format and translation library (OME-TIFF, Bio-Formats), data management software platforms, and microscopy metadata recommendations and annotation tools. Bringing these developments into practice requires support and training. Iterative feedback and tool improvement is needed to foster practical adoption by the scientific community. The Information Infrastructure for BioImage Data (I3D:bio) project works on guidelines, training resources, and practical assistance for FAIR microscopy RDM adoption with a focus on the management platform OMERO and metadata annotations.
Notes (English)
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202403_Poster_I3Dbio_GerBICommunity_share.pdf
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Additional details
References
- Kunis S, Hänsch S, Schmidt C. et al. (2021): MDEmic: a metadata annotation tool to facilitate management of FAIR image data in the bioimaging community. Nat Methods 18, 1416–1417, https://doi.org/10.1038/s41592-021-01288-z
- OMERO docs: https://omero-guides.readthedocs.io/en/latest/external_tools.html
- Schmidt C, Hanne J, et al. (2022): Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey. F1000Research, 11:638 (https://doi.org/10.12688/f1000research.121714.2), CC-BY 4.0 (http://creativecommons.org/licenses/by/4.0)
- Kunis S & Dohle J (2022): Structuring of Data and Metadata in Bioimaging: Concepts and technical Solutions in the Context of Linked Data. Zenodo. https://doi.org/10.5281/zenodo.7018750
- Schmidt, C., Bortolomeazzi, M., Boissonnet, T., Fortmann-Grote, C., Dohle, J., Zentis, P., Kandpal, N., Kunis, S., Zobel, T., Weidtkamp-Peters, S., & Ferrando-May, E. (2023): I3D:bio's OMERO training material: Re-usable, adjustable, multi-purpose slides for local user training. Zenodo. https://doi.org/10.5281/zenodo.8323588 (a) + YouTube Video Tutorials https://www.youtube.com/playlist?list=PL2k-L-zWPoR7SHjG1HhDIwLZj0MB_stlU (b)
- Sarkans U, Chiu W, Collinson L, et al. (2021): REMBI: Recommended Metada for Biological Images - enabling reuse of microscopy data. Nat Methods 18, 1418-1422, https://doi.org/10.1038/s41592-021-01166-8