Display options
Cite
Hammer M, Huisman M, Rigano A, et al. Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. Nat Methods. 2021;18(12):1427-1440doi: 10.1038/s41592-021-01327-9.
Hammer, M., Huisman, M., Rigano, A., Boehm, U., Chambers, J. J., Gaudreault, N., North, A. J., Pimentel, J. A., Sudar, D., Bajcsy, P., Brown, C. M., Corbett, A. D., Faklaris, O., Lacoste, J., Laude, A., Nelson, G., Nitschke, R., Farzam, F., Smith, C. S., Grunwald, D., & Strambio-De-Castillia, C. (2021). Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. Nature methods, 18(12), 1427-1440. https://doi.org/10.1038/s41592-021-01327-9
Hammer, Mathias, et al. "Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model." Nature methods vol. 18,12 (2021): 1427-1440. doi: https://doi.org/10.1038/s41592-021-01327-9
Hammer M, Huisman M, Rigano A, Boehm U, Chambers JJ, Gaudreault N, North AJ, Pimentel JA, Sudar D, Bajcsy P, Brown CM, Corbett AD, Faklaris O, Lacoste J, Laude A, Nelson G, Nitschke R, Farzam F, Smith CS, Grunwald D, Strambio-De-Castillia C. 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. PMID: 34862501.
Copy Download .nbib Format: NLM
Share it on

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

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

Nature methods

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

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 BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University 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. [email protected].

PMID: 34862501 DOI: 10.1038/s41592-021-01327-9

[No abstract available.]

References

  1. Dekker, J. et al. Nature 549, 219–226 (2017). - PubMed
  2. 4D Nucleome Consortium. The 4D Nucleome Web Portal. https://www.4dnucleome.org/ (2017) - PubMed
  3. Strambio-De-Castillia, C. et al. Quality Control and Data Management | Bioimaging North America (BINA). Bioimaging North America https://www.bioimagingna.org/qc-dm-wg (2019). - PubMed
  4. BioImaging North America. https://www.bioimagingna.org (2018) - PubMed
  5. Hammer, M. et al. Preprint at bioRxiv https://doi.org/10.1101/2021.05.31.446382 (2021). - PubMed
  6. Huisman, M. et al. Preprint at https://arxiv.org/abs/1910.11370 (2021). - PubMed
  7. Huisman, M. et al. Preprint at https://arxiv.org/abs/1910.11370v3 (2019) - PubMed
  8. Goldberg, I. G. et al. Genome Biol. 6, R47 (2005). - PubMed
  9. Linkert, M. et al. J. Cell Biol. 189, 777–782 (2010). - PubMed
  10. Ram, S. & Liu, J. J. Data Semant. 1, 11–17 (2012). - PubMed
  11. Boehm, U. et al. Nat. Methods https://doi.org/10.1038/s41592-021-01162-y (2021). - PubMed
  12. Nelson, G. et al. J. Microsc. https://doi.org/10.1111/jmi.13041 (2021). - PubMed
  13. Nelson, G. et al. Preprint at http://arxiv.org/abs/2101.09153 (2021). - PubMed
  14. Rigano, A. et al. 4DN-BINA-OME (NBO) Tiered Microscopy Metadata Specifications - v2.01. https://github.com/WU-BIMAC/NBOMicroscopyMetadataSpecs (2021); https://doi.org/10.5281/zenodo.4710731 - PubMed
  15. Kunis, S. et al. Nat. Methods https://doi.org/10.1038/s41592-021-01288-z (2021). - PubMed
  16. Rigano, A. et al. Nat. Methods https://doi.org/10.1038/s41592-021-01315-z (2021). - PubMed
  17. Ryan, J. et al. Nat. Methods https://doi.org/10.1038/s41592-021-01290-5 (2021). - PubMed
  18. Rigano, A. et al. Preprint at bioRxiv https://doi.org/10.1101/2021.05.31.446382 (2021). - PubMed
  19. Ryan, J. et al. Preprint at bioRxiv https://doi.org/10.1101/2021.06.23.449674 (2021). - PubMed
  20. Kunis, S. et al. Preprint at http://arxiv.org/abs/2103.02942 (2021). - PubMed
  21. Baker, M. Nature 533, 452–454 (2016). - PubMed
  22. Marqués, G., Pengo, T. & Sanders, M. A. eLife 9, e55133 (2020). - PubMed
  23. Sheen, M. R. et al. eLife 8, e45120 (2019). - PubMed
  24. Viana, M. P. et al. Preprint at bioRxiv https://doi.org/10.1101/2020.12.08.415562 (2021). - PubMed
  25. Botvinik-Nezer, R. et al. Nature 582, 84–88 (2020). - PubMed
  26. Nature Editorial Staff. Nat. Methods 15, 395 (2018). - PubMed
  27. Pines, J. Open Biol. 10, 200165 (2020). - PubMed
  28. Wilkinson, M. D. et al. Sci. Data 3, 160018 (2016). - PubMed
  29. Allan, C. et al. Nat. Methods 9, 245–253 (2012). - PubMed
  30. Swedlow, J. R., Goldberg, I., Brauner, E. & Sorger, P. K. Science 300, 100–102 (2003). - PubMed
  31. Wittner, R. et al. in Provenance and Annotation of Data and Processes. International Provenance and Annotation Workshop (IPAW) 2020–2021 (eds. Glavic, B., Braganholo, V. & Koop, D.) 222–225 (Springer, 2021). - PubMed
  32. Holub, P. et al. Preprint at Zenodo https://doi.org/10.5281/zenodo.5093125 (2021). - PubMed
  33. Kobayashi, N. et al. in Proceedings of the 12th Annual SWAT4(HC)LS (Semantic Web Applications and Tools for Healthcare and Life Sciences) Conference (CEUR Workshop Proceedings, vol. 2849) (eds. Cornet, R. & Waagmeester, A.) 149–150 (2019); http://ceur-ws.org/Vol-2849/paper-25.pdf - PubMed
  34. Moore, J. et al. in Proceedings of the 12th SWAT4(HC)LS Conference (CEUR Workshop Proceedings, vol. 2849) (eds. Cornet, R. & Waagmeester, A.) 44–53 (2019); http://ceur-ws.org/Vol-2849/paper-06.pdf - PubMed
  35. Hammer, M. et al. in Proceedings of the 12th Annual SWAT4(HC)LS Conference (CEUR Workshop Proceedings, vol. 2849) (eds. Cornet, R. & Waagmeester, A.) 153–154 (2019); http://ceur-ws.org/Vol-2849/paper-27.pdf - PubMed
  36. Moore, J. et al. Preprint at bioRxiv https://doi.org/10.1101/2021.03.31.437929 (2021). - PubMed
  37. Moore, J. et al. OME-NGFF: a next-generation file format for expanding bioimaging data access strategies. Nat. Methods https://doi.org/10.1038/s41592-021-01326-w (in the press). - PubMed
  38. Deutsch, E. W. et al. Nat. Biotechnol. 26, 305–312 (2008). - PubMed
  39. Brazma, A. ScientificWorldJournal 9, 420–423 (2009). - PubMed
  40. Rigano, A. & Strambio-De-Castillia, C. Preprint at bioRxiv https://doi.org/10.1101/155036 (2017). - PubMed
  41. Miura, K. & Nørrelykke, S. F. EMBO J. 40, e105889 (2021). - PubMed
  42. Masuzzo, P. Minimum Information About Cell Migration Experiments (MIACME 0.2) (2021); https://cmso.science/MIACME/v0.2/ - PubMed
  43. North, A. J. J. Cell Biol. 172, 9–18 (2006). - PubMed
  44. Theer, P., Mongis, C. & Knop, M. Nat. Methods 11, 981–982 (2014). - PubMed
  45. Lambert, T. J. & Waters, J. C. Methods Cell Biol. 123, 35–53 (2014). - PubMed
  46. Deagle, R. C., Wee, T. E. & Brown, C. M. Int. J. Biochem. Cell Biol. 89, 120–124 (2017). - PubMed
  47. Mubaid, F. et al. Histochem. Cell Biol. 151, 357–366 (2019). - PubMed
  48. Kiepas, A., Voorand, E., Mubaid, F., Siegel, P. M. & Brown, C. M. J. Cell Sci. 133, jcs242834 (2020). - PubMed
  49. Hill, E. J. Cell Biol. 183, 969–970 (2008). - PubMed
  50. Montero Llopis, P. et al. Nat. Methods https://doi.org/10.1038/s41592-021-01156-w (2021). - PubMed
  51. Heddleston, J. M., Aaron, J. S., Khuon, S. & Chew, T.-L. J. Cell Sci. 134, jcs254144 (2021). - PubMed
  52. Aaron, J. S. & Chew, T.-L. J. Cell Sci. 134, jcs254144 (2021). - PubMed
  53. Williams, E. et al. Nat. Methods 14, 775–781 (2017). - PubMed
  54. Ellenberg, J. et al. Nat. Methods 15, 849–854 (2018). - PubMed
  55. Sarkans, U. et al. Nat. Methods https://doi.org/10.1038/s41592-021-01166-8 (2021). - PubMed
  56. Swedlow, J. R. et al. Nat. Methods https://doi.org/10.1038/s41592-021-01113-7 (2021). - PubMed
  57. Iudin, A., Korir, P. K., Salavert-Torres, J., Kleywegt, G. J. & Patwardhan, A. Nat. Methods 13, 387–388 (2016). - PubMed
  58. Guilbert, T. Cochin Image Database (2019); https://imagerie.cochin.inserm.fr/sis4web/login.php - PubMed
  59. Orloff, D. N., Iwasa, J. H., Martone, M. E., Ellisman, M. H. & Kane, C. M. Nucleic Acids Res. 41, D1241–D1250 (2013). - PubMed
  60. Tohsato, Y., Ho, K. H. L., Kyoda, K. & Onami, S. Bioinformatics 32, 3471–3479 (2016). - PubMed
  61. Hammer, M. et al. 4DN-BINA-OME (NBO) Microscopy Metadata Specs - Tiers System - v2.01. https://github.com/WU-BIMAC/NBOMicroscopyMetadataSpecs/tree/master/Tier%20System/stable%20version/v02-01 (2021); https://doi.org/10.5281/zenodo.4710731 - PubMed
  62. Chen, P. P.-S. ACM Trans. Database Syst. 1, 9–36 (1976). - PubMed
  63. Rigano, A. & Strambio-De-Castillia, C. 4DN-BINA-OME (NBO) Tiered Microscopy Metadata Specifications - v2.01 - XSD schema. Zenodo https://doi.org/10.5281/zenodo.4711426 (2021). - PubMed
  64. Rigano, A. et al. 4DN-BINA-OME (NBO) Tiered Microscopy Metadata Specifications - v2.01 - XLS Spreadsheet and Entity Relationship schemas. Zenodo https://doi.org/10.5281/zenodo.4711229 (2021). - PubMed
  65. Bradner, S. Key words for use in RFCs to indicate requirement levels [RFC2119] (1997); http://www.ietf.org/rfc/rfc2119.txt - PubMed
  66. Reiff, S. B. et al. Preprint at bioRxiv https://doi.org/10.1101/2021.10.14.464435 (2021) - PubMed
  67. de Souza, N. Nat. Methods 9, 1046 (2012). - PubMed
  68. Movincell Consortium. Multi-dimensional marine organism dataview. Movincell (2015); http://movincell.org/ - PubMed
  69. Allen Institute for Cell Science. Allen Cell Explorer (2017); https://www.allencell.org/ - PubMed
  70. Rozenblatt-Rosen, O. et al. Nat. Biotechnol. 39, 149–153 (2021). - PubMed
  71. HuBMAP Consortium. The Human BioMolecular Atlas Program - HuBMAP (2017); https://hubmapconsortium.org/ - PubMed
  72. DORY Working Group. Defining Our Research Methodology (2019); https://doryworkspace.org/ - PubMed
  73. Sansone, S.-A. et al. OMICS 12, 143–149 (2008). - PubMed
  74. Ioannidis, J. P. A. et al. Nat. Genet. 41, 149–155 (2009). - PubMed
  75. Rung, J. & Brazma, A. Nat. Rev. Genet. 14, 89–99 (2013). - PubMed
  76. Grebnev, G. & Global BioImaging. Global BioImaging training resource (2021); https://globalbioimaging.org/international-training-courses/repository - PubMed
  77. Waters, J., Jug, F., Elliott, H. & Lambert, T. Cold Spring Harbor Laboratory courses: Quantitative imaging: from acquisition to analysis. Cold Spring Harbor Laboratory (2021); https://meetings.cshl.edu/courses.aspx?course=C-QICM&year=21 - PubMed
  78. North, A. & Bewersdorf, J. Marine Biology Laboratory courses: optical microscopy & imaging in the biomedical sciences (OMIBS). University of Chicago Marine Biological Laboratory (2021); https://www.mbl.edu/education/courses/optical-microscopy-imaging/ - PubMed
  79. Allen, L., O’Connell, A. & Kiermer, V. Learn. Publ. 32, 71–74 (2019). - PubMed

Publication Types

Grant support