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  • PhD Student
  • Physician
  • Post-doc
  • Prize
  • Project Manager
  • Research Associate
  • Research Engineer
  • Retired scientist
  • Technician
  • Undergraduate Student
  • Veterinary
  • Visiting Scientist
  • Deputy Director of Center
  • Deputy Director of Department
  • Deputy Director of National Reference Center
  • Deputy Head of Facility
  • Director of Center
  • Director of Department
  • Director of Institute
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Scientific Fields
Diseases
Organisms
Applications
Technique

About

The lab is focused on the algorithms and computation selected by evolution to perform biological decision-making. We address this topic with an interdisciplinary approach mixing statistical physics, Bayesian machine learning, information theory and various experimental biological setups.

 

Former Members

2000
2000
Name
Position
2017
2018
Sandrine Clais
Administrative Staff
2018
2018
Nicolas Skatchkovsky
Graduate Student
2017
2019
Sébastien Doutreligne
Research Engineer
2019
2019
Maxime Duval
Graduate Student
2020
2020
Till Kletti
Graduate Student
2019
2021
Thomas Blanc
Graduate Student
2017
2020
Alexander Serov
Post-doc
2018
2020
Tihana Jovanic
postdoc
2020
2021
Valentin Marcon
Engineer
2017
2021
Mohamed el Beheiry
postdoctoral fellow & CTO of Avatar Medical
2019
2022
Hippolyte Verdier
PhD student
2018
2022
Corentin guerinot
PhD student
Show all

Jobs

M1/M2 internship: Signature of out-of-equilibrium dynamics in a partially observed system

M1/M2 internship: Signature of out-of-equilibrium dynamics in a partially observed system There are numerous challenges in statistically testing whether a dynamic system displays out-of-equilibrium dynamics from experimental recordings.  Commonly, we have access to only […]

M1/M2 internship: Single particle tracking with structured illumination

M1/M2 internship: Single particle tracking with structured illumination Super-resolved localization microscopy and single particle tracking (SPT) have become stable techniques of molecular biophysics, and are providing unprecedented insights into the spatio-temporal organization and biomolecular […]

M1/M2 Internship: Topology of neural connectomes

M1/M2 Internship: Topology of neural connectomes Behavior and decision-making are determined by physical processes taking place in the complex environment of the brain. Experimental techniques have reached the point where it is now possible […]

Projects

Project
Ongoing
7 Members

Deciding in Complex environments

Jean-Baptiste Masson (PI)

This project aims at understanding the dynamical behaviour of drosophila larva. The larva is a ~10000 neurons that exhibit complex behaviour dynamics in response to external stimuli and to possible internal states. This project is […]
Project
Ongoing
5 Members

Topological and statistical properties of neural connectomes

Christian L. Vestergaard (PI)

This project aims to characterize the mircrociruit structure of small animals’ brains and link this to how the brain processes information and encodes behavior.  The project relies on simultaneous access to recent synapse-resolution wiring […]
Project
Ongoing
7 Members

Modelling and diagnosing fetuses

Jean-Baptiste Masson (PI)

Improvements of fetal diagnosis allow now addressing complex diseases through multimodal procedures. However, there are known limitations to what can be accurately diagnosed from ultrasound and complementary invasive tests may have side effects. Complementary […]
Project
Ongoing
3 Members

Numerical methods for network analysis

Christian L. Vestergaard (PI)

Networks provide an efficient formalism to study many complex real-world systems. They provide a natural modeling framework of structural and functional brain networks, protein interaction networks, social interactions, information and epidemic spreading, and infrastructural […]
Project
Ongoing
6 Members

Semi-automatic transfer function for virtual reality

Mohamed El Beheiry (PI)
Project
Ongoing
6 Members

Mapping Receptor Dynamics In Synapses

François Laurent (PI)

This project aims at understanding the synaptic environment at the single receptor scale. Now that large amounts of dynamical single molecule data are available and that single molecule science is slowly transitioning into a big […]
Project
Completed
9 Members

DIVA — Data Integration and Visualisation in Augmented and Virtual Environments

Jean-Baptiste Masson (PI)

A Unique Software Platform for Complex Image Analysis Using Virtual Reality         DIVA (Data Integration and Visualization in Augmented and Virtual Environments)  is a software platform jointly developed by the Decision and Bayesian […]
Project
Completed
5 Members

Congenital heart disease

Francesca Raimondi (PI)

  Congenital heart surgery is a challenging surgical disciplines due to the broad spectrum of conditions and high variability of patient anatomies. Extensive understanding of the complex spatial relationship between anatomical structures is mandatory […]

Transversal Project

Brain connectivity and neurodegenerative diseases

The brain is a complex organ, and its well-being depends on the harmonic interactions with the rest of our body. Nearly all brain disorders manifest themselves in the dysfunction of communication between brain cells […]

Cancer Initiative

With more than 19.3 million new cases in 2020 worldwide, including nearly 400,000 in France, cancer is a common disease that affects or will affect us all one day, directly or indirectly. It is […]

INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations

IINCEPTION Goal The Inception aims to develop a core structure to mobilize data resources, numerical sciences, and fundamental experimental biology in various health issues (Official website here: https://www.inception-program.fr/en). The inception program uses Integrative Biology, […]

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 […]

Software

Software
Not started
7 Members

Themis, Nyx, Japet & Héméré

François Laurent (PI)

Themis, Nyx, Japet & Héméré are the four software we will be developing starting in 2022 Themis will be a Julia library that generates greedy decision making from probability distribution of relevant summary statistics. […]
Software
Ongoing
6 Members

TRamWAy

François Laurent (PI)

Single-molecule localization microscopy (SMLM) allows studying the dynamics of molecules in cells and resolving the biophysical properties that underlie cellular function. With the continuously growing amount of data produced by every single experiment, the […]
Software
Completed
5 Members

Genuage platform

Jean-Baptiste Masson (PI)

Genuage is a new open-source software platform, that enables the easy perception of, interaction with and analysis of multidimensional point clouds in virtual reality. Genuage is compatible with arbitrary multidimensional data and allows easy […]
Software
Completed
6 Members

DIVA microscopy

Jean-Baptiste Masson (PI)

DIVA is a software platform that enhances the analysis of biomedical and microscopy images using virtual reality. It virtually places users inside rich 3D environments based on their experimentally acquired imaging data. Highly interactive, it […]
Software
Completed
2 Members

Escale

François Laurent (PI)
Software
Completed
3 Members

InferenceMAP

Jean-Baptiste Masson (PI)

InferenceMAP  is a software aimed at analysing single molecule dynamics. InferenceMAP is based on Bayesian analysis of Random Walks and this version is focused on mapping Random Walks at the full cell scale in […]
Software
Ongoing
3 Members

Palmari

Jean-Baptiste Masson (PI)

Palmari is a Python package allowing one to process PALM (photo-activated localization microscopy) movies in order to extract trajectories. The documentation can be found online : https://palmari.readthedocs.io/en/latest/ It has two entry points : it […]

Patents

Method and device for monitoring detection of odours by moving animals or by moving apparatus in turbulent flows

This patent consist on the combine use of electronics and antenna of insects to measure odour on moving systems (alive or not). It allows the measure of odour paths. An example of odour path […]

Method, device, and computer program for locating an emitting source

The patent consists on a computational biomimetic strategy to search for cue emitting sources in turbulent flows. An example of implementation can be seen on the following video with a robot searching for a thermal source. […]

Fundings

Partners

Publications

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Former or Completed Projects

Jean-Baptiste Masson
Head of Structure
François Laurent
Research Engineer
Christian L. Vestergaard
Permanent Researcher

Congenital heart disease

  Congenital heart surgery is a challenging surgical disciplines due to the broad spectrum of conditions and high variability of patient anatomies. Extensive understanding of the complex spatial relationship between anatomical structures is mandatory […]

Mapping Receptor Dynamics In Synapses

This project aims at understanding the synaptic environment at the single receptor scale. Now that large amounts of dynamical single molecule data are available and that single molecule science is slowly transitioning into a big […]

DIVA — Data Integration and Visualisation in Augmented and Virtual Environments

A Unique Software Platform for Complex Image Analysis Using Virtual Reality         DIVA (Data Integration and Visualization in Augmented and Virtual Environments)  is a software platform jointly developed by the Decision and Bayesian […]

Pictures & Media

Chloe Barre’s interventions during the round table about Neuro and AI at C-brain inauguration day.

 

From left to right: Alain Destexhe, Chloé Barre, Brice Bathellier,Joelle Barral et  AlAlexandre Gramfort

Imabio Workshop: Image Treatment in Virtual Reality

Visualisation and Analysis of Large Microscopy Images in Virtual Reality

The beginning of DIVA 

Colloque Génération IA 2030

Surgery planning with Virtual Reality and Machine learning