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Jean-Marie Burel

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Burel, Jean-Marie

Dr

 https://orcid.org/0000-0002-1789-1861
20042026

Research activity per year

Personal profile

Biography

Jean-Marie studied Mathematics and obtained a PhD in Differential Geometry.
He was a post-doctoral researcher at the University of Lund before joining the group of Prof Jason Swedlow in early 2003 to work on imaging challenges.

Research

Imaging is one of the most innovative and widely used technologies in modern life sciences research.
He has been part of the Open Microscopy Environment (OME) since its creation in 2003 by Professor Jason Swedlow. OME is an open-source technology development effort to build the data management and integration tools needed to make imaging data a first-class resource for the next generation of life sciences research.  OME develops and releases data models, file format translators and data management software.
OME's flagship tools Bio-Formats and OMERO are used daily by both academic and industry communities.

We have used Bio-Formats and OMERO to build the Image Data Resource (IDR), one of the largest public bioimaging data repositories in the world. IDR publishes bioimaging datasets associated with peer reviewed publications. The flexibility provided by Bio-Formats and OMERO means that IDR can handle a wide range of data types from research domains across the life and biomedical sciences. The IDR project collaborates with the EMBL-EBI’s Bioimage Archive and RIKEN’s SSBD database to construct a larger ecosystem for public bioimaging data. Several projects worldwide now use the technology constructed for IDR for publishing their own data.

We are part of a consortium combining software developers with experimental biologists, imaging scientists using many different modalities, and data repository experts who will collaborate to design and deliver the next generation of data format technologies e.g. OME-NGFF, OME-Zarr for use by the global imaging community.

In recent years, I have played a leading role on FAIR and sustainability initiatives as part of the EOSC-Life project. I currently lead OME’s efforts in various UK programmes aiming to improve FAIR practices within scientific communities.

Education/Academic qualification

Doctor of Philosophy, Structures géométriques sur les variétés et applications harmoniques, Université de Bretagne Occidentale

Award Date: 15 Sept 2000

Keywords

  • QA76 Computer software
  • Q Science (General)

Expertise related to UN Sustainable Development Goals

In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):

  1. SDG 3 - Good Health and Well-being
    SDG 3 Good Health and Well-being
  2. SDG 4 - Quality Education
    SDG 4 Quality Education
  3. SDG 5 - Gender Equality
    SDG 5 Gender Equality

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Collaborations and top research areas from the last five years

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  • Building capacity in imaging data management

    Velasquez, S. M., Fletcher, G., Burel, J. M., Parsons, M., Swedlow, J., Hartley, M., Bagia, S., Beckett, A., Crichton, J. H., Cross, S. J., Foulkes, D. M., Grimshaw, J., Held, M., Ho, K., Jones, M., Lee, M., Marcello, M., Marcotti, S., Markus, R. & McConnell, G. & 4 others, Thomas, S. G., West, S. J., Wheeler, A. & Küpcü Yoldaş, A. (Lead / Corresponding author), Jun 2026, In: Journal of Microscopy. 302, 3, p. 334-345 12 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    11 Downloads (Pure)

  • IDR searcher: a search engine solution for public image resources

    Mohamed, K., Moore, W., Lindner, D., Moore, J., Swedlow, J. R., Walczysko, P., Wong, F. & Burel, J.-M. (Lead / Corresponding author), 1 Jul 2026, In: Bioinformatics. 42, 7, 8 p., btag486.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    7 Downloads (Pure)

  • Search, organize, aggregate and share image data with BioFile Finder (BFF)

    Meharry, S. L. (Lead / Corresponding author), Borensztejn, A., Gaudreault, N., Lucas, J., Medrash, G., Schaefbauer, L., Toloudis, D., Wallace, A., Whitney, B., Wilhelm, L., Ben-Simon, Y., Burel, J. M., Chen, J., Eliceiri, K. W., Grüneboom, A., Kyoda, K., Moore, J., Moore, W., Onami, S. & Panzeri, D. & 3 others, Rueden, C. T., Tasic, B. & Johnson, G. T. (Lead / Corresponding author), 15 Jun 2026, In: Nature Methods.

    Research output: Contribution to journal › Letter › peer-review

    2   Link opens in a new tab Citations (Scopus)

  • bia-binder: a web-native cloud compute service for the bioimage analysis community

    Russell, C. T., Burel, J. M., Athar, A., Li, S., Sarkans, U., Swedlow, J., Brazma, A., Hartley, M. (Lead / Corresponding author) & Uhlmann, V. (Lead / Corresponding author), Aug 2025, In: Bioinformatics. 41, 8, 5 p., btaf412.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    53 Downloads (Pure)

  • OME-Zarr: a cloud-optimized bioimaging file format with international community support

    Moore, J. (Lead / Corresponding author), Basurto-Lozada, D., Besson, S., Bogovic, J., Bragantini, J., Brown, E. M., Burel, J.-M., Casas Moreno, X., de Medeiros, G., Diel, E. E., Gault, D., Ghosh, S. S., Gold, I., Halchenko, Y. O., Hartley, M., Horsfall, D., Keller, M. S., Kittisopikul, M., Kovacs, G. & Küpcü Yoldaş, A. & 49 others, Kyoda, K., le Tournoulx de la Villegeorges, A., Li, T., Liberali, P., Lindner, D., Linkert, M., Lüthi, J., Maitin-Shepard, J., Manz, T., Marconato, L., McCormick, M., Lange, M., Mohamed, K., Moore, W., Norlin, N., Ouyang, W., Özdemir, B., Palla, G., Pape, C., Pelkmans, L., Pietzsch, T., Preibisch, S., Prete, M., Rzepka, N., Samee, S., Schaub, N., Sidky, H., Solak, A. C., Stirling, D. R., Striebel, J., Tischer, C., Toloudis, D., Virshup, I., Walczysko, P., Watson, A. M., Weisbart, E., Wong, F., Yamauchi, K. A., Bayraktar, O., Cimini, B. A., Gehlenborg, N., Haniffa, M., Hotaling, N., Onami, S., Royer, L. A., Saalfeld, S., Stegle, O., Theis, F. J. & Swedlow, J. R., Sept 2023, In: Histochemistry and Cell Biology. 160, p. 223–251 29 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    75   Link opens in a new tab Citations (Scopus)
    224 Downloads (Pure)
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  • 1 Participation in workshop, seminar, course