Bioimage Informatics – From microscopy to quantitative biology

Host: Bertrand Vernay

Abstract

Modern developments in light microscopy have shed light on a wide range of phenomena occurring around and inside cells, with remarkable spatiotemporal resolution and reproducibility, posing a significant challenge in visualising and extracting relevant information from this sheer amount of imaging data. This talk will focus on some of the recent developments in the field of Bioimage Informatics, dedicated to the production of algorithms and software for advanced image acquisition, processing and quantification. I shall first highlight some recent efforts toward the quantification of cellular morpho-dynamics, for which we develop a repertoire of computational approaches to a) automatically track cells in 2D/3D environments, b) efficiently describe the cell morphology to extract spatiotemporal deformation patterns, and c) extract biophysical quantities at the intra-cellular level directly from imaging data alone. I shall then discuss the important issue of bridging the gap between the computer vision and biology communities, by facilitating the distribution of advanced tools to the community in the form of user-friendly, open-source software, notably through the development of Icy, the next-generation bioimaging platform (http://icy.bioimageanalysis.org).

Short Bio

Alexandre Dufour graduated in artificial intelligence and pattern recognition in 2004 from Paris Pierre & Marie Curie University (France), and obtained the Ph.D. degree in image processing in 2007 from Paris Descartes University (France). From 2005 to 2007 he was a Junior Scientist at the Institut Pasteur of Seoul (South Korea), developing pioneering algorithms for 3D High-Content-Screening applications. In 2008 he joined the group of Jean-Christophe Olivo-Marin at the Institut Pasteur of Paris (France) and became a Permanent Staff Scientist in 2011, leading a research pole in the group on cell motility and dynamics. In 2014 he was a Visiting Scientist at Imperial College London working on the dynamics of Plasmodia with Bob Sinden and Jake Baum, and returned to Institut Pasteur Paris in 2015 where he was appointed Senior Staff Scientist, studying the mechanics of cell deformation and migration though a combination of cell biology, microscopy, and image analysis techniques. He is also actively involved in the development of open-source software development for reproducible research in the Bioimage Informatics community.