David Pinto
Senior Research Software Engineer at University of Oxford, Department of Engineering Science
Oxford, England, United Kingdom
Summary
👤
Senior🎓
Top SchoolDavid Pinto is a Senior Research Software Engineer in Oxford with 16 years of experience at the intersection of computer vision, microscopy control, and biology. He combines a PhD-level understanding of biochemistry with hands-on engineering, shipping image analysis algorithms and microscope automation for academic imaging facilities. A core developer and maintainer in GNU Octave and contributor to prominent projects like Bio-Formats and CodaLab Competitions, he balances low-level file-format fixes with full-stack web and UI improvements. His work spans languages and stacks—from Java and Perl for bioinformatics to web security hardening and Octave-compatible algorithm refactors—reflecting a practical, cross-disciplinary approach. Active in open source communities, he often takes on leadership, maintenance, and support roles rather than only feature work. Colleagues rely on him to translate complex biological imaging needs into robust, reproducible software.
16 years of coding experience
4 years of employment as a software developer
Applied Biology, Molecular Biology, Microbiology, Plant Biology, Applied Biology, Molecular Biology, Microbiology, Plant Biology at Universidade do MinhoDoctor of Philosophy - PhD, Biochemistry, Doctor of Philosophy - PhD, Biochemistry at National University of Ireland, Galway
English, Portuguese, Spanish, French
Stackoverflow
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Github Skills (35)
tournament10
biom10
python10
image-processing10
scripting10
django10
bioperl10
formatter10
matlab10
environment-variables10
perl10
java10
javas10
toolkits10
formatters10
Programming languages (23)
Github contributions (5)
bioperl/bioperl-live
Jul 2011 - Sep 2019
Core BioPerl 1.x code
Role in this project:
Backend Developer
Backend DeveloperContributions:196 commits, 11 PRs, 122 pushes in 8 years 3 months
Contributions summary:David's commits focused on modifying Perl scripts within the BioPerl-live repository, specifically addressing script documentation and file permissions. The user corrected script names, updated documentation to match the new naming conventions, and reset file permissions to a standard state. These changes suggest a focus on code quality, documentation, and maintenance for the existing BioPerl scripts, particularly the command-line clients.
bioperlpdb-filesbiologytoolkitbioinformatics
ome/bioformats
Jul 2014 - Dec 2019
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:31 commits, 14 PRs, 46 comments in 5 years 5 months
Contributions summary:David primarily worked on improving the `PGMReader` within the `bioformats` library, addressing issues related to image file format parsing, specifically for Netpbm files. They fixed bugs related to header parsing and comment handling and added support for more file extensions. Additionally, the user refactored the MATLAB code, adjusting it for Octave compatibility and resolving versioning issues.
gnubammetadatabio-formatscommercial
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