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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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  • ORCID record for Maximiliaan Huisman
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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  • ORCID record for Damir Sudar
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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  • ORCID record for Alexander D. Corbett
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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  • ORCID record for Carlas S. Smith
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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Article Information

doi 
https://doi.org/10.1101/2021.04.25.441198
History 
  • April 26, 2021.

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  • Version 2 (April 28, 2021 - 23:52).
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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.

Author Information

  1. Mathias Hammer*,1,
  2. Maximiliaan Huisman*,1,
  3. Alex Rigano*,2,
  4. Ulrike Boehm#,3,
  5. James J. Chambers#,4,
  6. Nathalie Gaudreault#,5,
  7. Alison J. North#,6,
  8. Jaime A. Pimentel#,7,
  9. Damir Sudar#,8,
  10. Peter Bajcsy#,9,
  11. Claire M. Brown#,10,
  12. Alexander D. Corbett#,11,
  13. Orestis Faklaris#,12,
  14. Judith Lacoste#,13,
  15. Alex Laude#,13,
  16. Glyn Nelson#,14,
  17. Roland Nitschke#,15,
  18. Farzin Farzam1,
  19. Carlas S. Smith16,
  20. David Grunwald1 and
  21. Caterina Strambio-De-Castillia#,2,*
  1. 1RNA Therapeutics Institute, UMass Medical School, Worcester MA 01605, USA
  2. 2Program in Molecular Medicine, UMass Medical School, Worcester MA 01605, USA
  3. 3Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
  4. 4Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA 01003, USA
  5. 5Allen Institute for Cell Science, Seattle, WA 98109, USA
  6. 6The Rockefeller University, New York, NY 10065, USA
  7. 7Instituto de Biotecnologıa, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, 62210, México
  8. 8Quantitative Imaging Systems LLC, Portland, OR 97209, USA
  9. 9National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
  10. 10Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, H3G 0B1, Canada
  11. 11Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QL, UK
  12. 12BCM, Univ. Montpellier, CNRS, INSERM, Montpellier, France
  13. 13MIA Cellavie Inc., Montreal, Quebec, H1K 4G6, Canada
  14. 14Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
  15. 15Life Imaging Center and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
  16. 16Delft Center for Systems and Control & Department of Imaging Physics, Delft University of Technology, Delft, 2628 CN, The Netherlands
  1. ↵* Corresponding author; email: caterina.strambio{at}umassmed.edu
  1. ↵* Contributed equally to this work

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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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