Towards community-driven metadata standards for light microscopy: tiered guidelines extending the OME model

Published

December 1, 2021

Author(s)

Peter Bajcsy, Mathias Hammer, Maximiliaan Huisman, Alex Rigano, Ulrike Boehm, James J. Chambers, Nathalie Gaudreault, Jaime A. Pimentel, Damir Sudar, Claire M. Brown, Alexander D. Corbett, Orestis Faklaris, Judith Lacoste, Alex Laude, Glyn Nelson, Roland Nitschke, Alison J. North, Renu Gopinathan, Farzin Farzam, Carlas Smith, David Grunwald, Caterina Strambio-De-Castillia

Abstract

While the power of modern microscopy techniques is undeniable, rigorous record-keeping and quality control are required to ensure that imaging data may be properly interpreted (quality), reproduced (reproducibility), and used to extract reliable information and scientific knowledge which can be shared for further analysis (value). In the absence of agreed guidelines, it is inherently difficult for scientists to create comprehensive records of imaging experiments and ensure the quality of resulting image data or for manufacturers to incorporate standardized reporting and performance metrics. To solve this problem, the 4D Nucleome (4DN) Initiative and BioImaging North America (BINA) here propose light Microscopy Metadata specifications that scale with experimental intent and with the complexity of the instrumentation and analytical requirements. They consist of a set of three extensions of the Open Microscopy Environment (OME) Data Model, and because of their tiered nature, they clearly specify which provenance and quality control metadata should be recorded for a given experiment. Last but not least, this endeavor is closely aligned with the undertakings of the recently established global community initiative dedicated to Quality Assessment and Reproducibility in Light Microscopy (QUAREP-LiMi; quarep.org). As a result the ensuing flexible 4DN-BINA-OME (NBO) framework represents a turning point towards achieving community-driven Microscopy Metadata standards that would increase data fidelity, improve repeatability and reproducibility, ease future analysis and facilitate the verifiable comparison of different datasets, experimental setups, and assays. The intention of this proposal is to encourage participation, critiques and contributions from the entire imaging community and all stakeholders, including research and imaging scientists, facility personnel, instrument manufacturers, software developers, standards organizations, journals and funding agencies.

Citation

Nature Methods

Volume

18

Pub Type

Journals

Download Paper

DOI Link

Keywords

metadata, microscopy, standards

Citation

Bajcsy, P. , Hammer, M. , Huisman, M. , Rigano, A. , Boehm, U. , Chambers, J. , Gaudreault, N. , Pimentel, J. , Sudar, D. , Brown, C. , Corbett, A. , Faklaris, O. , Lacoste, J. , Laude, A. , Nelson, G. , Nitschke, R. , North, A. , Gopinathan, R. , Farzam, F. , Smith, C. , Grunwald, D. and Strambio-De-Castillia, C. (2021), Towards community-driven metadata standards for light microscopy: tiered guidelines extending the OME model, Nature Methods, [online], https://doi.org/10.1038/s41592-021-01327-9 (Accessed October 13, 2025)