Jean-marie Burel
Independent Investigator
Dundee, Scotland, United Kingdom
Summary
👤
Senior🎓
Top SchoolJean-marie Burel is a senior bioinformatics researcher and software architect with 16+ years building and leading development of the OME ecosystem, including flagship projects Bio-Formats and OMERO. Based in Dundee, he combines a PhD-level mathematical background with hands-on engineering across the full stack, designing scalable APIs, distributed storage and parallel algorithms for large-scale bioimaging. He has driven data model and XML schema refactors in the widely used Bio-Formats library and improved robust image-download tooling in Galaxy-related projects, showing a practical commitment to interoperable open-source science. As a senior manager he has overseen local and distributed teams while maintaining day-to-day contributions and infrastructure ownership. He also bridges research and production: from harmonic morphism research in early postdoc work to delivering software used by thousands of scientists worldwide. His uncommon blend of deep mathematics, long-term stewardship of community software, and low-level data-format expertise makes him effective at solving both theoretical and operational imaging-data challenges.
16 years of coding experience
Doctor of Philosophy - PhD Mathematics, Doctor of Philosophy - PhD Mathematics at Université de Bretagne OccidentaleMaster's degree Mathematics, Master's degree Mathematics at University of Montpellier
French, English
Github Skills (11)
xml10
javas10
data-conversion10
toolz10
wrapper10
python10
toolbox10
java10
xslt10
image-processing9
error-handling9
Programming languages (23)
Github contributions (5)
ome/bioformats
Aug 2009 - Oct 2022
Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
Role in this project:
Back-end Developer
Back-end DeveloperContributions:16 reviews, 367 commits, 71 PRs in 13 years 4 months
Contributions summary:Jean-marie primarily contributed to refactoring the existing code base and modifying the structure of XML transformation files within the Bio-Formats project. The commits involved rewriting XML namespaces, renaming attributes and elements, and handling the conversion of older schema versions to the latest versions. These changes suggest that the user was heavily involved in the project's data model and ensuring its compatibility with various data formats and schema versions.
gnubammetadatabio-formatscommercial
galaxyproject/tools-iuc
Feb 2020 - Apr 2020
Tool Shed repositories maintained by the Intergalactic Utilities Commission
Role in this project:Back-end Developer
Back-end DeveloperContributions:6 commits, 2 PRs, 7 comments in 2 months
Contributions summary:Jean-marie primarily contributed to the `idr_download_by_ids.py` tool, focusing on functionality related to image downloading and processing. Their work involved adding channel retrieval logic, incorporating case-insensitive comparisons, and implementing error handling for more robust operations. The user also made adjustments to ensure the downloaded regions can be properly specified and handled.
intergalacticrepositoriesusegalaxywrapperscommission
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