Jean-Marie Burel

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Burel, Jean-Marie

Dr

 https://orcid.org/0000-0002-1789-1861
Calculated based on number of publications stored in Pure and citations from Scopus
20042025

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.

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):

  • SDG 3 - Good Health and Well-being
  • SDG 4 - Quality Education
  • SDG 5 - Gender Equality

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)

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  • 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), 22 Jul 2025, In: Bioinformatics. 41, 8, btaf412.

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

    Open Access
    File

  • 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
    45 Citations (Scopus)
    174 Downloads (Pure)

  • “Be sustainable”: EOSC-Life recommendations for implementation of FAIR principles in life science data handling

    David, R., Rybina, A., Burel, J.-M., Hériché, J.-K., Audergon, P., Boiten, J.-W., Coppens, F., Crockett, S., Exter, K., Fahrner, S., Fratelli, M., Goble, C., Gormanns, P., Grantner, T., Grüning, B., Gurwitz, K. T., Hancock, J. M., Harmse, H., Holub, P. & Juty, N. & 39 others, Karnbach, G., Karoune, E., Keppler, A., Klemeier, J., Lancelotti, C., Legras, J. L., Lister, A. L., Longo, D. L., Ludwig, R., Madon, B., Massimi, M., Matser, V., Matteoni, R., Mayrhofer, M. T., Ohmann, C., Panagiotopoulou, M., Parkinson, H., Perseil, I., Pfander, C., Pieruschka, R., Raess, M., Rauber, A., Richard, A. S., Romano, P., Rosato, A., Sánchez-Pla, A., Sansone, S. A., Sarkans, U., Serrano-Solano, B., Tang, J., Tanoli, Z., Tedds, J., Wagener, H., Weise, M., Westerhoff, H. V., Wittner, R., Ewbank, J. (Lead / Corresponding author), Blomberg, N. (Lead / Corresponding author) & Gribbon, P. (Lead / Corresponding author), 1 Dec 2023, In: EMBO Journal. 42, 23, 23 p., e115008.

    Research output: Contribution to journal › Comment/debate › peer-review

    Open Access
    File
    15 Citations (Scopus)

  • OME-NGFF: a next-generation file format for expanding bioimaging data access strategies

    Moore, J., Allan, C., Besson, S., Burel, J.-M., Diel, E., Gault, D., Kozlowski, K., Lindner, D., Linkert, M., Manz, T., Moore, W., Pape, C., Tischer, C. & Swedlow, J. R. (Lead / Corresponding author), Dec 2021, In: Nature Methods. 18, p. 1496-1498 3 p.

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

    Open Access
    File
    95 Citations (Scopus)
    178 Downloads (Pure)

  • Bringing Open Data to Whole Slide Imaging

    Besson, S., Leigh, R., Linkert, M., Allan, C., Burel, J.-M., Carroll, M., Gault, D., Gozim, R., Li, S., Lindner, D., Moore, J., Moore, W., Walczysko, P., Wong, F. & Swedlow, J. (Lead / Corresponding author), 2019, Digital Pathology: 15th European Congress, ECDP 2019, Warwick, UK, April 10–13, 2019, Proceedings. Reyes-Aldasoro, C. C., Janowczyk, A., Veta, M., Bankhead, P. & Sirinukunwattana, K. (eds.). Switzerland: Springer , p. 3-10 8 p. (Lecture Notes in Computer Science; vol. 11435).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access
    File
    26 Citations (Scopus)
    406 Downloads (Pure)
View all 17 research outputs