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CITATION.cff
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# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: 4DN-BINA-OME Microscopy Metadata Specifications
message: >-
If you use this specifications, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Mathias
affiliation: >-
RNA Therapeutic Institute, UMass Chan Medical
School, Worcester MA 01605, USA
family-names: Hammer
- given-names: Huisman
affiliation: ' RNA Therapeutic Institute, UMass Chan Medical School, Worcester MA 01605, USA'
orcid: 'https://orcid.org/0000-0003-3363-8791'
family-names: Maximiliaan
- given-names: Alessandro
family-names: Rigano
email: [email protected]
affiliation: >-
Program in Molecular Medicine, UMass Chan
Medical School, Worcester MA 01605, USA
- given-names: Ulrike
affiliation: >-
Janelia Research Campus, Howard Hughes Medical
Institute, Ashburn, VA 20147, USA
orcid: 'https://orcid.org/0000-0001-7471-2244'
family-names: Boehm
- given-names: James
affiliation: >-
Institute for Applied Life Sciences, University
of Massachusetts, Amherst, MA 01003, USA
orcid: 'https://orcid.org/0000-0003-3883-8215'
family-names: Chambers
- given-names: Nathalie
affiliation: >-
Allen Institute for Cell Science, Seattle, WA
98109, USA
family-names: Gaudreault
orcid: 'https://orcid.org/0000-0002-9220-5366'
- given-names: Alison J.
affiliation: >-
The Rockefeller University, New York, NY 10065,
USA
orcid: 'https://orcid.org/0000-0002-0577-7949'
family-names: North
- given-names: Arturo
affiliation: >-
Instituto de Biotecnologıa, Universidad
Nacional Autonoma de Mexico, Cuernavaca,
Morelos, 62210, México
orcid: 'https://orcid.org/0000-0001-8569-0466'
family-names: Pimentel
- given-names: Damir
affiliation: >-
Quantitative Imaging Systems LLC, Portland, OR
97209, USA
orcid: 'https://orcid.org/0000-0002-2510-7272'
family-names: 'Sudar '
- given-names: Peter
affiliation: >-
National Institute of Standards and Technology,
Gaithersburg, MD 20899, USA
orcid: 'https://orcid.org/0000-0002-6968-2615'
family-names: 'Bajcsy '
- given-names: Claire M.
affiliation: >-
Advanced BioImaging Facility (ABIF), McGill
University, Montreal, Quebec, H3G 0B1, Canada
orcid: 'https://orcid.org/0000-0003-1622-663X'
family-names: Brown
- given-names: Alexander D.
affiliation: >-
Department of Physics and Astronomy, University
of Exeter, Exeter, EX4 4QL, UK
orcid: 'https://orcid.org/0000-0003-1645-5475'
family-names: Corbett
- given-names: Orestis
affiliation: >-
Biocampus, CNRS UMS 3426, Montpellier 34293,
France
orcid: 'https://orcid.org/0000-0001-5965-5405'
family-names: Faklaris
- given-names: Judith
affiliation: >-
MIA Cellavie Inc., Montreal, Quebec, H1K 4G6,
Canada
family-names: Lacoste
orcid: 'https://orcid.org/0000-0002-8783-8599'
- given-names: Alex
affiliation: >-
Bioimaging Unit, Newcastle University,
Newcastle upon Tyne, NE2 4HH, UK
orcid: 'https://orcid.org/0000-0002-3853-1187'
family-names: Laude
- given-names: Glyn
affiliation: >-
Bioimaging Unit, Newcastle University,
Newcastle upon Tyne, NE2 4HH, UK
orcid: 'https://orcid.org/0000-0002-1895-4772'
family-names: Nelson
- given-names: Roland
affiliation: >-
Life Imaging Center and BIOSS Centre for
Biological Signaling Studies,
Albert-Ludwigs-University Freiburg, Freiburg,
79104, Germany
orcid: 'https://orcid.org/0000-0002-9397-8475'
family-names: Nitschke
- given-names: Farzin
affiliation: >-
RNA Therapeutic Institute, UMass Chan Medical
School, Worcester MA 01605, USA
family-names: Farzam
- given-names: Carlas S.
affiliation: >-
Dutch Optics Center, Technische Universiteit
Delft, Delft, 2600 AA, The Netherlands
family-names: Smith
orcid: 'https://orcid.org/0000-0003-0591-5093'
- given-names: 'David '
affiliation: >-
RNA Therapeutic Institute, UMass Chan Medical
School, Worcester MA 01605, USA
family-names: Grunwald
orcid: 'https://orcid.org/0000-0001-9067-804X'
- affiliation: >-
Program in Molecular Medicine, UMass Chan
Medical School, Worcester MA 01605, USA
orcid: >-
https://orcid.org/https://orcid.org/0000-0002-1069-1816
family-names: Strambio-De-Castillia
given-names: Caterina
email: [email protected]
repository-code: >-
https://github.com/WU-BIMAC/NBOMicroscopyMetadataSpecs
url: 'https://doi.org/10.5281/zenodo.4710731'
abstract: >-
This is a proposal put forth by the 4D Nucleome
(4DN) Imaging Standards Working Group and by the
Bioimaging North America (BINA) Quality Control and
Data Management Working Group for a suite of
extensions of the OME data model schema which was
originally released in June 2016 by the Open
Microscopy Environment
keywords:
- metadata
- microscopy
- standards
- data model
- OME
- open science
- reproducibility
- quality control
- data provenance
- 4D Nucleome
- Microscope-hardware-specifications
- Image-acquisition-settings
- metadata specifications
license: GPL-3.0-or-later
version: '2.01'
date-released: '2021-04-12'
references:
- authors:
- family-names: Mathias
given-names: Hammer
affiliation: RNA Therapeutic Institute, University of Massachusetts Chan Medical School
- family-names: Maximiliaan
given-names: Huisman
affiliation: RNA Therapeutic Institute, University of Massachusetts Chan Medical School
orcid: https://orcid.org/0000-0003-3363-8791
- family-names: Rigano
given-names: Alessandro
affiliation: Program in Molecular Medicine, University of Massachusetts Chan Medical School
- family-names: Boehm
given-names: Ulrike
affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
orcid: https://orcid.org/0000-0001-7471-2244
- family-names: Chambers
given-names: James
affiliation: Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA 01003, USA
orcid: https://orcid.org/0000-0003-3883-8215
- family-names: Gaudreault
given-names: Nathalie
affiliation: Allen Institute for Cell Science, Seattle, WA 98109, USA
- family-names: North
given-names: Alison J.
affiliation: The Rockefeller University, New York, NY 10065, USA
orcid: https://orcid.org/0000-0002-0577-7949
- family-names: Pimentel
given-names: Arturo
affiliation: Instituto de Biotecnologıa, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, 62210, México
orcid: https://orcid.org/0000-0001-8569-0466
- family-names: Sudar
given-names: Damir
affiliation: Quantitative Imaging Systems LLC, Portland, OR 97209, USA
orcid: https://orcid.org/0000-0002-2510-7272
- family-names: Bajcsy
given-names: Peter
affiliation: National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
orcid: https://orcid.org/0000-0002-6968-2615
- family-names: Brown
given-names: Claire M.
affiliation: Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, H3G 0B1, Canada
orcid: https://orcid.org/0000-0003-1622-663X
- family-names: Corbett
given-names: Alexander D.
affiliation: Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QL, UK
orcid: https://orcid.org/0000-0003-1645-5475
- family-names: Faklaris
given-names: Orestis
affiliation: Biocampus, CNRS UMS 3426, Montpellier 34293, France
orcid: https://orcid.org/0000-0001-5965-5405
- family-names: Lacoste
given-names: Judith
affiliation: MIA Cellavie Inc., Montreal, Quebec, H1K 4G6, Canada
- family-names: Laude
given-names: Alex
affiliation: Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
orcid: https://orcid.org/0000-0002-3853-1187
- family-names: Nelson
given-names: Glyn
affiliation: Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
orcid: http://orcid.org/0000-0002-1895-4772
- family-names: Nitschke
given-names: Roland
affiliation: Life Imaging Center and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
orcid: https://orcid.org/0000-0002-9397-8475
- family-names: Gopinathan
given-names: Renu
affiliation: RNA Therapeutics Institute, UMass Medical School, Worcester MA 01605, USA
- family-names: Farzam
given-names: Farzin
affiliation: RNA Therapeutics Institute, UMass Medical School, Worcester MA 01605, USA
- family-names: Carlas
given-names: Smith
affiliation: Dutch Optics Center, Technische Universiteit Delft, Delft, 2600 AA, The Netherlands
- family-names: David
given-names: Grunwald
affiliation: University of Massachusetts Medical School
- family-names: Strambio-De-Castillia
given-names: Caterina
affiliation: University of Massachusetts Medical School
email: [email protected]
orcid: https://orcid.org/0000-0002-1069-1816
doi: 10.1101/2021.04.25.441198
journal: "BioRxiv.org"
scope: "Cite this paper every time you use these specifications."
title: "Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model"
type: article
year: 2021
- authors:
- family-names: Maximiliaan
given-names: Huisman
affiliation: University of Massachusetts Medical School
- family-names: Mathias
given-names: Hammer
affiliation: University of Massachusetts Medical School
orcid: https://orcid.org/0000-0003-3363-8791
- family-names: Rigano
given-names: Alessandro
affiliation: University of Massachusetts Medical School
- family-names: Boehm
given-names: Ulrike
affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
orcid: https://orcid.org/0000-0001-7471-2244
- family-names: Chambers
given-names: James
affiliation: Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA 01003, USA
orcid: https://orcid.org/0000-0003-3883-8215
- family-names: Gaudreault
given-names: Nathalie
affiliation: Allen Institute for Cell Science, Seattle, WA 98109, USA
- family-names: North
given-names: Alison J.
affiliation: The Rockefeller University, New York, NY 10065, USA
orcid: https://orcid.org/0000-0002-0577-7949
- family-names: Pimentel
given-names: Arturo
affiliation: Instituto de Biotecnologıa, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, 62210, México
orcid: https://orcid.org/0000-0001-8569-0466
- family-names: Sudar
given-names: Damir
affiliation: Quantitative Imaging Systems LLC, Portland, OR 97209, USA
orcid: https://orcid.org/0000-0002-2510-7272
- family-names: Bajcsy
given-names: Peter
affiliation: National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
orcid: https://orcid.org/0000-0002-6968-2615
- family-names: Brown
given-names: Claire M.
affiliation: Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, H3G 0B1, Canada
orcid: https://orcid.org/0000-0003-1622-663X
- family-names: Corbett
given-names: Alexander D.
affiliation: Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QL, UK
orcid: https://orcid.org/0000-0003-1645-5475
- family-names: Faklaris
given-names: Orestis
affiliation: Biocampus, CNRS UMS 3426, Montpellier 34293, France
orcid: https://orcid.org/0000-0001-5965-5405
- family-names: Lacoste
given-names: Judith
affiliation: MIA Cellavie Inc., Montreal, Quebec, H1K 4G6, Canada
- family-names: Laude
given-names: Alex
affiliation: Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
orcid: https://orcid.org/0000-0002-3853-1187
- family-names: Nelson
given-names: Glyn
affiliation: Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
orcid: http://orcid.org/0000-0002-1895-4772
- family-names: Nitschke
given-names: Roland
affiliation: Life Imaging Center and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
orcid: https://orcid.org/0000-0002-9397-8475
- family-names: David
given-names: Grunwald
affiliation: University of Massachusetts Medical School
- family-names: Strambio-De-Castillia
given-names: Caterina
affiliation: University of Massachusetts Medical School
email: [email protected]
orcid: https://orcid.org/0000-0002-1069-1816
url: https://arxiv.org/abs/1910.11370
journal: "arXiv.org"
scope: "Cite this paper every time you use these specifications."
title: "A perspective on Microscopy Metadata: data provenance and quality control"
type: article
year: 2021
- authors:
- family-names: Mathias
given-names: Hammer
affiliation: RNA Therapeutic Institute, University of Massachusetts Chan Medical School
- family-names: Maximiliaan
given-names: Huisman
affiliation: RNA Therapeutic Institute, University of Massachusetts Chan Medical School
orcid: https://orcid.org/0000-0003-3363-8791
- family-names: Rigano
given-names: Alessandro
affiliation: Program in Molecular Medicine, University of Massachusetts Chan Medical School
- family-names: Boehm
given-names: Ulrike
affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
orcid: https://orcid.org/0000-0001-7471-2244
- family-names: Chambers
given-names: James
affiliation: Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA 01003, USA
orcid: https://orcid.org/0000-0003-3883-8215
- family-names: Gaudreault
given-names: Nathalie
affiliation: Allen Institute for Cell Science, Seattle, WA 98109, USA
- family-names: North
given-names: Alison J.
affiliation: The Rockefeller University, New York, NY 10065, USA
orcid: https://orcid.org/0000-0002-0577-7949
- family-names: Pimentel
given-names: Arturo
affiliation: Instituto de Biotecnologıa, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, 62210, México
orcid: https://orcid.org/0000-0001-8569-0466
- family-names: Sudar
given-names: Damir
affiliation: Quantitative Imaging Systems LLC, Portland, OR 97209, USA
orcid: https://orcid.org/0000-0002-2510-7272
- family-names: Bajcsy
given-names: Peter
affiliation: National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
orcid: https://orcid.org/0000-0002-6968-2615
- family-names: Brown
given-names: Claire M.
affiliation: Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, H3G 0B1, Canada
orcid: https://orcid.org/0000-0003-1622-663X
- family-names: Corbett
given-names: Alexander D.
affiliation: Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QL, UK
orcid: https://orcid.org/0000-0003-1645-5475
- family-names: Faklaris
given-names: Orestis
affiliation: Biocampus, CNRS UMS 3426, Montpellier 34293, France
orcid: https://orcid.org/0000-0001-5965-5405
- family-names: Lacoste
given-names: Judith
affiliation: MIA Cellavie Inc., Montreal, Quebec, H1K 4G6, Canada
- family-names: Laude
given-names: Alex
affiliation: Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
orcid: https://orcid.org/0000-0002-3853-1187
- family-names: Nelson
given-names: Glyn
affiliation: Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
orcid: http://orcid.org/0000-0002-1895-4772
- family-names: Nitschke
given-names: Roland
affiliation: Life Imaging Center and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
orcid: https://orcid.org/0000-0002-9397-8475
- family-names: Gopinathan
given-names: Renu
affiliation: RNA Therapeutics Institute, UMass Medical School, Worcester MA 01605, USA
- family-names: Farzam
given-names: Farzin
affiliation: RNA Therapeutics Institute, UMass Medical School, Worcester MA 01605, USA
- family-names: Carlas
given-names: Smith
affiliation: Dutch Optics Center, Technische Universiteit Delft, Delft, 2600 AA, The Netherlands
- family-names: David
given-names: Grunwald
affiliation: University of Massachusetts Medical School
- family-names: Strambio-De-Castillia
given-names: Caterina
affiliation: University of Massachusetts Medical School
email: [email protected]
orcid: https://orcid.org/0000-0002-1069-1816
doi: 10.1038/s41592-021-01327-9
journal: "Nature Methods"
volume: 18
pages: 1428
scope: "Cite this paper every time you use these specifications."
title: "Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model"
type: article
year: 2021