Jean-Christophe Olivo-Marin is the Head of the BioImage Analysis unit and the director of the institute Carnot Pasteur Microbes et Santé. He chaired the Cell Biology and Infection Department (2010-2014) and was CTO and Director of the Center for Innovation and Technological Research (2015-2018). Previous to that, he was a staff scientist at the European Molecular Biology Laboratory, Heidelberg, from 1990 to 1998. He received the PhD and HDR degrees in optics and signal processing from the Institut d’Optique Théorique et Appliquée, University of Paris-Orsay, France. He is a Fellow of IEEE and of SPIE, an IEEE Signal Processing Society Distinguished Lecturer, and was Chair of the IEEE SPS Bio Imaging and Signal Processing Technical Committee (BISP-TC). His research interests are in image analysis of multidimensional microscopy images, computer vision and motion analysis for cellular dynamics, and in mathematical approaches for biological imaging.
INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations
IINCEPTION Goal The Inception’s goal is to develop a core structure to mobilize data resources, numerical sciences, and fundamental experimental biology in a range of health issues. Inception program uses Integrative Biology, Social Science […]
The Quantitative Biology program of the Institut Pasteur is intended to facilitate research and education at the interface of biology and the more quantitative sciences. One of the major aims of Quantitative Biology is thus to […]
Institut Carnot Pasteur MS
The Carnot Label Carnot label is granted to public research structures, showing high level R&D competencies dedicated to fostering innovation with industrial partners. The Carnot Institutes (IC) are funded to conduct upstream research capable […]
LabEx IBEID – Integrative Biology of Emerging Infectious Diseases
Presentation The aim of the Integrative Biology of Emerging Infectious Diseases (IBEID) project, coordinated by Professors Philippe Sansonetti and Pascale Cossart, is to develop a structure to anticipate and tackle emerging infectious diseases (EIDs). […]
Impact of gut mechanical forces and 3D architecture on the intestine homeostasis during pathogen interaction and in cancer disease
The intestine, and in particular the colon, comprising a mucus blanket, an epithelial monolayer and the lamina propria rich in immune cells, is constantly subjected to shear stress (flow) and peristaltic motion (stretching), both […]
Endothelium disruption by toxin-induced transcellular tunnels
Crossing of the epithelium and endothelium barriers by pathogens and their toxins represents essential steps in pejorative evolution of infections. We have discovered that several exotoxins from S. aureus and C. botulinum disrupt epithelium and endothelium barriers by targeting […]
DIM ELICIT – Domaine d’Intérêt Majeur “Empowering LIfe sCiences with Innovative Technologies”
Depuis le 15 décembre 2016, le DIM ELICIT est labellisé Domaines d’Intérêt Majeur par le Conseil régional d’Ile-de-France pour la période 2017-2020. Co-coordonné par l’Institut Pierre Gilles de Gennes (IPGG, Patrick Tabeling) et l’Institut […]
Welcome to the club! Welcome to Microfluidics@Pasteur! Our goal is to serve as the major entry point to all the scientists on the campus (beginners and experts) interested in undertaking projects where microfluidics is involved. Our […]
Protected: Pasteur Human Genome
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Compressive Sensing in biological imaging
We are investigating a new global framework for smart acquisition methods in biological imaging whereby it is possible with mathematical tools to recover a high quality image from very fewer samples than the full […]
Imaging and mathematical modelling of cell morphology and motility
Elucidating the mechanisms underlying cell deformation and motility is a topic of major interest in cell biology, for they are strongly involved in cell development, immune responses, cancer and infectious diseases. This projects focuses on the […]
Multiple spot tracking in 3D+t microscopy
We have developed a method to perform the detection and the tracking of microscopic spots directly on four dimensional (3D+t) image data. It extends our previous work by being able to detect with high […]
Color image analysis in histology
To characterize histopathological images stained by different colorations, we have developed a system to analyse color images. Images are segmented by a split and merge approach and by color quantization, to reduce color classes. We have also defined a criterion to choose […]
Private: Denoising of microscopic images: state-of-the-art techniques and shared database of images
State-of-the-art denoising techniques: Adapted to Gaussian Noise: Lee additive TV TV-LSE TV-ICE NLM BM3D 2. Adapted to Poisson Noise: Poisson EM-TV TV-ICE Poisson NLM-Poisson NLPCA 3. […]
Icy: an open community platform for bioimage informatics
We started a project for a new open-source image processing software platform dedicated to community work (de Chaumont et al, Nature Methods 2012). It includes a flexible framework designed around and with a native […]
2019Real-time analysis of the behaviour of groups of mice via a depth-sensing camera and machine learning, Nat Biomed Eng 2019 Nov;3(11):930-942.
2018Anisotropic organization of circumferential actomyosin characterizes hematopoietic stem cells emergence in the zebrafish, Elife 2018 08;7.
2018Denoising of Microscopy Images: A Review of the State-of-the-Art, and a New Sparsity-Based Method, IEEE Transactions on Image Processing, 2018, vol. 27, no 8, p. 3842-3856.
2017Crosstalk between Entamoeba histolytica and the human intestinal tract during amoebiasis, Parasitology 2017 Dec;:1-10.
2017An objective comparison of cell-tracking algorithms, Nat. Methods 2017 Dec;14(12):1141-1152.
2017A sparsity-based simplification method for segmentation of spectral-domain optical coherence tomography images, Proc. SPIE 10394, Wavelets and Sparsity XVII, 1039406 (24 August 2017); doi: 10.1117/12.2274126;.
2017BioFlow: a non-invasive, image-based method to measure speed, pressure and forces inside living cells, Sci Rep 2017 Aug;7(1):9178.
2017Activation of human gonadotropin-releasing hormone receptor promotes down regulation of ARHGAP18 and regulates the cell invasion of MDA-MB-231 cells, Mol. Cell. Endocrinol. 2018 Jan;460:94-103.
2017Deciphering tissue morphodynamics using bioimage informatics, Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2017 May;372(1720).
2017Reducing data acquisition for fast structured illumination microscopy using compressed sensing, 10.1109/ISBI.2017.7950461.
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