I am a researcher in the field of image analysis and computer vision applied to biology. My current positions:
- Director of the Centre for
Computational Biology (CBIO)
- Codirector of the department "Cancer and Genome: Bioinformatics, Biostatistics, Epidemiology of Complex Systems" (Institut Curie / Mines ParisTech / INSERM)
My research field is Bioimage Informatics, the branch of Computational
Biology concerned with the computational analysis of bioimages.
My most visible contributions have been in the field of computational phenotyping,
applied to High Content Screening (HCS).
I develop computer vision and machine learning methods to quantify
morphological changes, classify cellular states and spatial trajectories
from live cell imaging data with applications to systematic large-scale
studies of cellular processes such as cell division and cell migration.
These methods can also be used to find and phenotypically characterize new drugs.
More recently, I have become interested in the field of spatial transcriptomics where we want to systematically study the spatial aspects of gene expression. Methodologically this involves image simulation, point cloud clustering and classification. A second axis of my current research is the computational phenotyping of cells in their tissular context in histopathology data, a very competitive field with important clinical applications. From a methodological perspective, this involves deep learning and multiple instance learning in order to analyze very large, stained tumor sections used in the clinics for diagnostic purposes, such as metastasis detection or outcome prediction.
I also coordinate the workgroup on High Content Screening of France-Bioimaging , I am active in a number of courses on Machine Learning and Computer Vision for Biology all over Europe, and I am also one of two coordinators of the Bioimage analysis activities of the GDR ImaBio .
The Centre for Computational Biology is a
joint laboratory between
, one of the most prominent French engineering
schools, and Institut Curie
major hospital and research center dedicated to cancer. We benefit
from an exceptional scientific environment with immediate access to
experts and collaborators in biology and medicine enabling a
stimulating interdisciplinary exchange. The laboratory is located on
the Paris campus of Institut Curie, near Pantheon.