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

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

doi:10.1038/s41592-021-01327-9

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

Nat Methods. 2021 Dec;18(12):1427-1440. doi: 10.1038/s41592-021-01327-9.

Authors

Mathias Hammer^#^{1

2}, Maximiliaan Huisman^#¹, Alessandro Rigano^#³, Ulrike Boehm⁴, James J Chambers⁵, Nathalie Gaudreault⁶, Alison J North⁷, Jaime A Pimentel⁸, Damir Sudar⁹, Peter Bajcsy¹⁰, Claire M Brown¹¹, Alexander D Corbett¹², Orestis Faklaris¹³, Judith Lacoste¹⁴, Alex Laude¹⁵, Glyn Nelson¹⁵, Roland Nitschke¹⁶, Farzin Farzam¹, Carlas S Smith¹⁷, David Grunwald¹, Caterina Strambio-De-Castillia¹⁸

Affiliations

¹ RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, USA.
² Department of Biology, Technical University of Darmstadt, Darmstadt, Germany.
³ Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA.
⁴ Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
⁵ Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, USA.
⁶ Allen Institute for Cell Science, Seattle, WA, USA.
⁷ The Rockefeller University, New York, NY, USA.
⁸ Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
⁹ Quantitative Imaging Systems LLC, Portland, OR, USA.
¹⁰ National Institute of Standards and Technology, Gaithersburg, MD, USA.
¹¹ Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, Canada.
¹² Department of Physics and Astronomy, University of Exeter, Exeter, UK.
¹³ MRI, BCM, University of Montpellier, CNRS, INSERM, Montpellier, France.
¹⁴ MIA Cellavie Inc., Montreal, Quebec, Canada.
¹⁵ Bioimaging Unit, Newcastle University, Newcastle upon Tyne, UK.
¹⁶ Life Imaging Center and Signalling Research Centres CIBSS and BIOSS, University of Freiburg, Freiburg, Germany.
¹⁷ Delft Center for Systems and Control and Department of Imaging Physics, Delft University of Technology, Delft, the Netherlands.
¹⁸ Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA. caterina.strambio@umassmed.edu.

^# Contributed equally.

Abstract

Rigorous record-keeping and quality control are required to ensure the quality, reproducibility and value of imaging data. The 4DN Initiative and BINA here propose light Microscopy Metadata specifications that extend the OME data model, scale with experimental intent and complexity, and make it possible for scientists to create comprehensive records of imaging experiments.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Biomedical Research / organization & administration
Calibration
Data Collection
Data Mining / standards
Humans
Metadata*
Microscopy / instrumentation*
Microscopy / methods*
Microscopy / standards*
Quality Control
Reproducibility of Results
Societies, Scientific
Software
Systems Integration
User-Computer Interface

Abstract

Publication types

MeSH terms

Grants and funding