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  • Undergraduate Student
  • Veterinary
  • Visiting Scientist
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  • Deputy Head of Facility
  • Director of Center
  • Director of Department
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© Research

About

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.

Transversal Projects

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 […]

Quantitative biology

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). […]

Projects

project
Ongoing
6 Members

Impact of gut mechanical forces and 3D architecture on the intestine homeostasis during pathogen interaction and in cancer disease

Nathalie Sauvonnet (PI)

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 […]
project
Ongoing
7 Members

Endothelium disruption by toxin-induced transcellular tunnels

Emmanuel Lemichez (PI)

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 […]
project
Ongoing
4 Members

DIM ELICIT – Domaine d’Intérêt Majeur “Empowering LIfe sCiences with Innovative Technologies”

Jean-Christophe Olivo-Marin (PI)

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 […]
project
Ongoing
15 Members

Microfluidics@Pasteur

Samy Gobaa (PI)

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 […]
project
Ongoing
21 Members

Protected: Pasteur Human Genome

Thomas Bourgeron (PI)

There is no excerpt because this is a protected post.
project
Ongoing
2 Members

Compressive Sensing in biological imaging

Jean-Christophe Olivo-Marin (PI)

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 […]
project
Ongoing
6 Members

Imaging and mathematical modelling of cell morphology and motility

Alexandre Dufour (PI)

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 […]
project
Ongoing
4 Members

Multiple spot tracking in 3D+t microscopy

Jean-Christophe Olivo-Marin (PI)

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 […]
project
Ongoing
4 Members

Color image analysis in histology

Vannary Meas-Yedid Hardy (PI)

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 […]

Software

software
Ongoing
2 Members

Private: Denoising of microscopic images: state-of-the-art techniques and shared database of images

Jean-Christophe Olivo-Marin (PI)

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.   […]
software
Ongoing
6 Members

Icy: an open community platform for bioimage informatics

Stéphane Dallongeville (PI)

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 […]
software
ongoing
1 Member

PG-URE estimator

Jean-Christophe Olivo-Marin (PI)

The PG-URE estimator is a statistical tool that can be used to assess the performance of image denoising algorithms in presence of mixed Poisson-Gaussian noise. In the spirit of reproducible research, the Matlab code […]

Publications

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