Dr Jean-Marie Burel

Imaging is one of the most innovative and widely used technologies in modern life sciences research.
I have 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.

Selected publications

• bia-binder: a web-native cloud compute service for the bioimage analysis community https://academic.oup.com/bioinformatics/article/41/8/btaf412/8210087 (2025)
• “Be sustainable”: EOSC‐Life recommendations for implementation of FAIR principles in life science data handling https://www.embopress.org/doi/full/10.15252/embj.2023115008 (2023)
• OME-Zarr: a cloud-optimized bioimaging file format with international community support https://www.biorxiv.org/content/10.1101/2023.02.17.528834v4 (2023)
• OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies https://www.nature.com/articles/s41592-021-01326-w (2021)
• Bringing Open Data to Whole Slide Imaging https://link.springer.com/chapter/10.1007/978-3-030-23937-4_1 (2019)
• Publishing and sharing multi-dimensional image data with OMERO https://link.springer.com/article/10.1007/s00335-015-9587-6 (2015)
• OMERO: flexible, model-driven data management for experimental biology https://www.nature.com/articles/nmeth.1896
• Metadata matters: access to image data in the real world https://rupress.org/jcb/article/189/5/777/35828/Metadata-matters-access-to-image-data-in-the-real