Curriculum vitae - Projects & Research Interests - Publications - Software - Conference Calendar - Students - Misc
My personal research interests lie within the field of "bioimage informatics", ie. the development and application of machine learning, computer vision, and software development methodologies to ease the recognition and quantification of cells, tissues and other biological or biomedical "objects" in large-scale imaging datasets, and on the delivery of user-friendly softwares to help biologists/pathologists/computer scientists/etc. to exploit big imaging data, derive new knowledge, and support their findings and diagnoses.
Since October 2010, I am the initiator and scientific coordinator of the CYTOMINE project which lead to the development of the CYTOMINE open-source software platform, a "Google Maps"-like rich internet application for remote visualization, annotation and automated analysis of high-resolution, multi-gigapixels images.
See Cytomine page for related publications, and below for an illustration of some applications.
This research is about the design of generic methods for automatic image classification, retrieval, and semantic segmentation.
Indeed, as potential applications of image recognition technologies are multidinous, we seek to develop general-purpose methods for the recognition of various types
of images that share some visual regularities, without relying on too strong assumptions about patterns to recognize and acquisition
conditions, and without having to rely on domain experts to design specific features.
This book chapter (2013) summarizes our work where we combine ensemble of randomized decision trees with random extraction of subwindows (square patches) described by their raw pixel values.
Between January 2005 and October 2014, I was the GIGA Bioinformatics platform manager (scientific head: Prof. L. Wehenkel). In close collaboration with the Bioinformatics and Modeling research unit, this platform offers software development and data analysis services to academic (within the GIGA research center and beyond) as well as to industrial researchers. Its services include classification of biological/biomedical data (SELDI mass spectra, microarrays, clinical databases, ...) obtained from various medical instrumentation based on machine learning methods.
This activity lead to co-authorship of several journal papers (in Journal of Immunology, Proteomics, Annals of the rheumatic diseases, ...) in various application domains (inflammatory diseases, cancer, ...).