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

Mathias Hammer, View ORCID ProfileMaximiliaan Huisman, Alex Rigano, View ORCID ProfileUlrike Boehm, View ORCID ProfileJames J. Chambers, View ORCID ProfileNathalie Gaudreault, View ORCID ProfileAlison J. North, View ORCID ProfileJaime A. Pimentel, View ORCID ProfileDamir Sudar, View ORCID ProfilePeter Bajcsy, View ORCID ProfileClaire M. Brown, View ORCID ProfileAlexander D. Corbett, View ORCID ProfileOrestis Faklaris, Judith Lacoste, View ORCID ProfileAlex Laude, View ORCID ProfileGlyn Nelson, View ORCID ProfileRoland Nitschke, Farzin Farzam, View ORCID ProfileCarlas S. Smith, David Grunwald, View ORCID ProfileCaterina Strambio-De-Castillia
doi: https://doi.org/10.1101/2021.04.25.441198
Mathias Hammer
1RNA Therapeutics Institute, UMass Medical School, Worcester MA 01605, USA
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Maximiliaan Huisman
1RNA Therapeutics Institute, UMass Medical School, Worcester MA 01605, USA
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Alex Rigano
2Program in Molecular Medicine, UMass Medical School, Worcester MA 01605, USA
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Ulrike Boehm
3Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
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James J. Chambers
4Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA 01003, USA
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Nathalie Gaudreault
5Allen Institute for Cell Science, Seattle, WA 98109, USA
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Alison J. North
6The Rockefeller University, New York, NY 10065, USA
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Jaime A. Pimentel
7Instituto de Biotecnologıa, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, 62210, México
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Damir Sudar
8Quantitative Imaging Systems LLC, Portland, OR 97209, USA
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Peter Bajcsy
9National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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Claire M. Brown
10Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, H3G 0B1, Canada
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Alexander D. Corbett
11Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QL, UK
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Orestis Faklaris
12BCM, Univ. Montpellier, CNRS, INSERM, Montpellier, France
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Judith Lacoste
13MIA Cellavie Inc., Montreal, Quebec, H1K 4G6, Canada
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Alex Laude
13MIA Cellavie Inc., Montreal, Quebec, H1K 4G6, Canada
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Glyn Nelson
14Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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Roland Nitschke
15Life Imaging Center and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
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Farzin Farzam
1RNA Therapeutics Institute, UMass Medical School, Worcester MA 01605, USA
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Carlas S. Smith
16Delft Center for Systems and Control & Department of Imaging Physics, Delft University of Technology, Delft, 2628 CN, The Netherlands
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David Grunwald
1RNA Therapeutics Institute, UMass Medical School, Worcester MA 01605, USA
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Caterina Strambio-De-Castillia
2Program in Molecular Medicine, UMass Medical School, Worcester MA 01605, USA
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  • ORCID record for Caterina Strambio-De-Castillia
  • For correspondence: caterina.strambio@umassmed.edu
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1 - ABSTRACT

Digital light microscopy provides powerful tools for quantitatively probing the real-time dynamics of subcellular structures. 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). Keeping notes on microscopy experiments and quality control procedures ought to be straightforward, as the microscope is a machine whose components are defined and the performance measurable. Nevertheless, to this date, no universally adopted community-driven specifications exist that delineate the required information about the microscope hardware and acquisition settings (i.e., microscopy “data provenance” metadata) and the minimally accepted calibration metrics (i.e., microscopy quality control metadata) that should be automatically recorded by both commercial microscope manufacturers and customized microscope developers. 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 add to the confusion, microscopy experiments vary greatly in aim and complexity, ranging from purely descriptive work to complex, quantitative and even sub-resolution studies that require more detailed reporting and quality control measures.

To solve this problem, the 4D Nucleome Initiative (4DN) (1,2) Imaging Standards Working Group (IWG), working in conjunction with the BioImaging North America (BINA) Quality Control and Data Management Working Group (QC-DM-WG) (3), 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 revision of the Core of the Open Microscopy Environment (OME) Data Model, which forms the basis for the widely adopted Bio-Formats library (4–6), accompanied by a suite of three extensions, each with three tiers, allowing the classification of imaging experiments into levels of increasing imaging and analytical complexity (7,8). Hence these specifications not only provide an OME-based comprehensive set of metadata elements that should be recorded, but they also specify which subset of the full list should be recorded for a given experimental tier. In order to evaluate the extent of community interest, an extensive outreach effort was conducted to present the proposed metadata specifications to members of several core-facilities and international bioimaging initiatives including the European Light Microscopy Initiative (ELMI), Global BioImaging (GBI), and European Molecular Biology Laboratory (EMBL) - European Bioinformatics Institute (EBI). Consequently, close ties were established between our endeavour and the undertakings of the recently established QUAlity Assessment and REProducibility for Instruments and Images in Light Microscopy global community initiative (9). As a result this flexible 4DN-BINA-OME (NBO namespace) framework (7,8) represents a turning point towards achieving community-driven Microscopy Metadata standards that will increase data fidelity, improve repeatability and reproducibility, ease future analysis and facilitate the verifiable comparison of different datasets, experimental setups, and assays, and it demonstrates the method for future extensions. Such universally accepted microscopy standards would serve a similar purpose as the Encode guidelines successfully adopted by the genomic community (10,11). The intention of this proposal is therefore 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, scientific publishers and funders.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵# Members of the Bioimaging North America Quality Control and Data Management Working Group

  • https://zenodo.org/record/4710731

  • https://zenodo.org/record/4711229

  • https://zenodo.org/record/4711426

  • Abbreviation list

    OME
    Open Microscopy Environment.
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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    Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model
    Mathias Hammer, Maximiliaan Huisman, Alex 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
    bioRxiv 2021.04.25.441198; doi: https://doi.org/10.1101/2021.04.25.441198
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    Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model
    Mathias Hammer, Maximiliaan Huisman, Alex 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
    bioRxiv 2021.04.25.441198; doi: https://doi.org/10.1101/2021.04.25.441198

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