WG 7 – Metadata
For proper interpretation, microscopy images must be accompanied by both human-readable (i.e., Materials and Methods sections) and machine-readable (i.e., metadata) descriptions of all steps leading to image formation (i.e., ‘data provenance’ metadata) as well as by QC metrics detailing the illumination, detection, chromatic, optical and mechanical performance of the microscope. Nevertheless, no universally accepted community guidelines exist defining what ‘data provenance’ and QC metadata should be reported for distinct types of imaging data. Therefore, the metadata automatically recorded by different commercial microscopes can vary widely, posing a substantial challenge for microscope users to create a bona fide record of their work. To meet these challenges, the 4D Nucleome (4DN) Imaging Working Group and the BINA QC-DM WG have developed a tiered set of Microscopy Metadata guidelines and a suite of extensions of the OME Data Model that scale with experimental complexity and requirements, and are specifically tailored at enhancing comparability and reproducibility in light microscopy. WG7 aims to systematically evaluate the structure and semantics of the initial 4DN-BINA-OME extension proposal and to launch a coordinated outreach strategy towards reaching a wide community consensus around the proposed metadata specifications.
- NBO Microscopy Metadata Specification ( formerly 4DN–BINA-OME Microscopy Metadata Model):
- Hammer, Mathias, Maximiliaan Huisman, Alessandro Rigano, Ulrike Boehm, James J. Chambers, Nathalie Gaudreault, Alison J. North, et al. “Towards Community-Driven Metadata Standards for Light Microscopy: Tiered Specifications Extending the OME Model.” Nature Methods, December 3, 2021, 1–14. https://doi.org/10.1038/s41592-021-01327-9. Cite
- Huisman, Maximiliaan, et al. “A perspective on Microscopy Metadata: data provenance and quality control.” arXiv, 24 Oct. 2019, arxiv.org/abs/1910.11370v6.
- How to provide feedback on the model
- Rigano, Alessandro, Shannon Ehmsen, Serkan Utku Öztürk, Joel Ryan, Alexander Balashov, Mathias Hammer, Koray Kirli, et al. “Micro-Meta App: An Interactive Tool for Collecting Microscopy Metadata Based on Community Specifications.” Nature Methods, December 3, 2021, 1–7. https://doi.org/10.1038/s41592-021-01315-z. Cite
- Ryan, Joel, Thomas Pengo, Alex Rigano, Paula Montero Llopis, Michelle S. Itano, Lisa A. Cameron, Guillermo Marqués, Caterina Strambio-De-Castillia, Mark A. Sanders, and Claire M. Brown. “MethodsJ2: A Software Tool to Capture Metadata and Generate Comprehensive Microscopy Methods Text.” Nature Methods, October 15, 2021, 1–3. https://doi.org/10.1038/s41592-021-01290-5. Cite
- GitHub (OMERO.mde implementation)
- Kunis, Susanne, Sebastian Hänsch, Christian Schmidt, Frances Wong, Caterina Strambio-De-Castillia, and Stefanie Weidtkamp-Peters. “MDEmic: A Metadata Annotation Tool to Facilitate Management of FAIR Image Data in the Bioimaging Community.” Nature Methods, October 11, 2021, 1–2. https://doi.org/10.1038/s41592-021-01288-z. Cite