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About

Academic background

During his PhD in robotics (Amiens, Berck), FdC conceived an autonomous robot designed to help disabled people, and especially paraplegics. The robot used omnidirectional vision sensor to SLAM and navigated automatically in the environment in order to follow the wheelchair of disabled people. The aim of the project was to deport heavy devices such as synthetic arm on the robot, and to make it a handy companion.

Projects

 Image analysis software – Icy

Fabrice de Chaumont was initially hired at Pasteur to create a 3D engine based on OpenGL to represent bio sample and image analysis results in the internal software of the unit. Then he designed a new image analysis software, Icy, created to offer the last developments of image analysis units to the biologist community. Icy is open source, based on plugins and receive contribution from different labs over the world. He wrote the base of the kernel of Icy and the website. Then Stephane Dallongeville joined the effort and is now leading the project. Important contributions, such as graphical programming and a number of additional contribution have been developed by Alexandre Dufour. Icy was published in Nature Methods in 2012. (Icy: an open bioimage informatics platform for extended reproducible research, Fabrice de Chaumont, Stéphane Dallongeville, Nicolas Chenouard, Nicolas Hervé, Sorin Pop, Thomas Provoost, Vannary Meas-Yedid, Praveen Pankajakshan, Timothée Lecomte, Yoann Le Montagner, Thibault Lagache, Alexandre Dufour & Jean-Christophe Olivo-Marin)

Fabrice de Chaumont also organised events such as the coding party of Icy covering (watch below)

He also initiated the Icy club, where people can come to solve original image analysis problem or get assistance on Icy (watch below). He is now contributing to Icy by developing advanced projects to the platform.

 

Mice tracking

In 2012, Fabrice de Chaumont was working on tracking C. elegans in screening scenario. He created a new tracking based on deformable models driven by physics engine but it has been finally applied to another field: as he met Sylvie Granon who works on behavioural analysis of mice. They applied the tracking model to mice tracking which allows behavioural understanding of the animals: it provides details during the contact of animals that cannot be labelled automatically before. It also enables the observation of the events’ dynamic. This method allows to provide much more data per animal observed, therefore contributes to reduce the number of animals needed for experiments.

 

 

This work was published in 2012 in Nature methods. (Computerized video analysis of social interactions in mice, Fabrice de Chaumont, Renata Dos-Santos Coura, Pierre Serreau, Arnaud Cressant, Jonathan Chabout, Sylvie Granon & Jean-Christophe Olivo-Marin). The software is available here.

Fabrice de Chaumont is currently working on a complete new solution dedicated to the tracking of animals in collaboration with Elodie Ey, member of the team Human genetics and cognitive functions (Thomas Bourgeron) and the team Neurophysiologiy and behaviour (Philippe Faure, Nicolas Torquet).

Particle/Spot detection and Tracking

Fabrice de Chaumont wrote the plugin Spot detector based on the method developed by Jean-Christophe Olivo-Marin. During Nicolas Chenouard‘s PhD he helped writing the analysis tools of tracks. He co-organized the tracking challenge in 2012 at ISBI. This challenge allowed leading teams in particle tracking to track generated images and to have a common metric to score methods depending on simulated scenario, with various noise and density of particle. The challenge was published in 2014 in Nature Methods. (Objective comparison of particle tracking methods. Nicolas Chenouard1, Ihor Smal1, Fabrice de Chaumont1, Martin Maška1, Ivo F. Sbalzarini, Yuanhao Gong, Janick Cardinale, Craig Carthel, Stefano Coraluppi, Mark Winter, Andrew R. Cohen, William J. Godinez, Karl Rohr, Yannis Kalaidzidis, Liang Liang, James Duncan, Hongying Shen, Yingke Xu, Klas E. G. Magnusson, Joakim Jaldén, Helen M. Blau, Perrine Paul-Gilloteaux, Philippe Roudot, Charles Kervrann, François Waharte, Jean-Yves Tinevez, Spencer L. Shorte, Joost Willemse, Katherine Celler, Gilles P. van Wezel, Han-Wei Dan, Yuh-Show Tsai, Carlos Ortiz de Solórzano, Jean-Christophe Olivo-Marin, Erik Meijering. Nature Methods, vol. 11, no. 3, pp. 281-289, March 2014) 1: co-first authors.

Web research at Pasteur

Fabrice de Chaumont is a member of the Secretariat Général Scientifique (Nathalie de Parseval), and is dedicated to the website research of Pasteur

Full list of publication available in google scholar

Events

Training – Icy software (Image Analysis)

Building: 6 – Room: 4 – Address: Institut Pasteur, Rue du Docteur Roux, Paris, France
2017-02-07 09:30:00 2017-02-07 16:30:00 Europe/Paris Training – Icy software (Image Analysis) The Bio Image Analysis unit organizes a training for Icy software : http://icy.bioimageanalysis.org Icy is an image analysis software connected to a web platform. It offers many image analysis tools including spot detection, tracking, […] Institut Pasteur, Rue du Docteur Roux, Paris, France

Solutions for Open Science

Building: François Jacob – Room: Amphithéâtre François Jacob – Address: Institut Pasteur, Rue du Docteur Roux, Paris, France
2017-10-11 00:00:00 2017-10-12 00:00:00 Europe/Paris Solutions for Open Science Venez découvrir des réalisations ou projets de prototypes d’instrumentation scientifique innovante au cours des journées thématiques organisées par le FabLab de l’Institut Pasteur et le groupe “Prototypes et Pilotage de Périphériques” du RT-MFM. Des […] Institut Pasteur, Rue du Docteur Roux, Paris, France

Courses

Digital Image Processing/Analysis Tools for Quantitative Light Microscopy Imaging

A 5-day practical course, scheduled to take place at the Hellenic Pasteur Institute, Athens Greece, in July 4-8, 2016, with objective to provide theoretical and practical training in basic and advanced concepts and methods […]

2016-07-04 15:53:16 2016-04-08 Europe/Paris Digital Image Processing/Analysis Tools for Quantitative Light Microscopy Imaging A 5-day practical course, scheduled to take place at the Hellenic Pasteur Institute, Athens Greece, in July 4-8, 2016, with objective to provide theoretical and practical training in basic and advanced concepts and methods […] Vasilissis Sofias avenue, 11521, athens

Projects

Publications