jean-baptiste Masson

jean-baptiste Masson
Institut Pasteur · Department of Neuroscience, C3BI

PhD

About

141
Publications
12,951
Reads
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2,284
Citations
Citations since 2017
52 Research Items
1514 Citations
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2017201820192020202120222023050100150200250300
2017201820192020202120222023050100150200250300
2017201820192020202120222023050100150200250300
Additional affiliations
February 2017 - present
Institut Pasteur
Position
  • Principal Investigator
September 2014 - September 2016
Janelia Farm Research Campus
Position
  • Visiting research specialist
January 2014 - June 2014
Institut Curie
Position
  • visiting scientist

Publications

Publications (141)
Article
Full-text available
Microscopy image observation is commonly performed on 2D screens, which limits human capacities to grasp volumetric, complex, and discrete biological dynamics. With the massive production of multidimensional images (3D + time, multi-channels) and derived images (e.g., restored images, segmentation maps, and object tracks), scientists need appropria...
Preprint
Full-text available
To coordinate cellular physiology, eukaryotic cells rely on the inter-organelle transfer of molecules at specialized organelle-organelle contact sites. Endoplasmic reticulum-mitochondria contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signaling molecules, lipids, and metabolites. ERMCSs are mai...
Article
Motivation: Single-molecule localization microscopy allows studying the dynamics of biomolecules in cells and resolving the biophysical properties of the molecules and their environment underlying cellular function. With the continuously growing amount of data produced by individual experiments, the computational cost of quantifying these properti...
Preprint
Full-text available
Numerous models have been developed to account for the complex properties of the random walks of biomolecules. However, when analysing experimental data, conditions are rarely met to ensure model identification. The dynamics may simultaneously be influenced by spatial and temporal heterogeneities of the environment, out-of-equilibrium fluxes and co...
Preprint
We introduce a simulation-based, amortised Bayesian inference scheme to infer the parameters of random walks. Our approach learns the posterior distribution of the walks' parameters with a likelihood-free method. In the first step a graph neural network is trained on simulated data to learn optimized low-dimensional summary statistics of the random...
Article
Full-text available
Hematopoietic stem cell transplantation (HSCT) is a therapy used for multiple malignant and nonmalignant diseases, with chemotherapy used for pretransplantation myeloablation. The post-HSCT brain contains peripheral engrafted parenchymal macrophages, despite their absence in the normal brain, with the engraftment mechanism still undefined. Here we...
Article
A combination of Bayesian inference, physics modeling, and Markov chain Monte Carlo sampling allows for accurate inference of biomolecule numbers and their photophysical state in cellular clusters.
Article
Full-text available
Three-dimensional imaging is at the core of medical imaging and is becoming a standard in biological research. As a result, there is an increasing need to visualize, analyze and interact with data in a natural three-dimensional context. By combining stereoscopy and motion tracking, commercial virtual reality (VR) headsets provide a solution to this...
Article
Full-text available
Multiple fields in biological and medical research produce large amounts of point cloud data with high dimensionality and complexity. In addition, a large set of experiments generate point clouds, including segmented medical data or single-molecule localization microscopy. In the latter, individual molecules are observed within their natural cellul...
Chapter
Based on the detection of individually fluorescing molecules, localization microscopy (LM) is currently an established imaging modality in studies of cellular biology. Applied to live cells, LM provides the means to probe environments with single molecule precision and, moreover, provide information on elementary biological processes. High-speed LM...
Article
Full-text available
Deviations from Brownian motion leading to anomalous diffusion are found in transport dynamics from quantum physics to life sciences. The characterization of anomalous diffusion from the measurement of an individual trajectory is a challenging task, which traditionally relies on calculating the trajectory mean squared displacement. However, this ap...
Article
PURPOSE The treatment of breast cancer, the leading cause of cancer and cancer mortality among women worldwide, is mainly on the basis of surgery. In this study, we describe the use of a medical image visualization tool on the basis of virtual reality (VR), entitled DIVA, in the context of breast cancer tumor localization among surgeons. The aim of...
Article
Full-text available
Background and Aim of the Study We sought to evaluate the appropriateness of cardiac anatomy renderings by a new virtual reality (VR) technology, entitled DIVA, directly applicable to raw magnetic resonance imaging (MRI) data without intermediate segmentation steps in comparison to standard three‐dimensional (3D) rendering techniques (3D PDF and 3D...
Preprint
Full-text available
Observed across species, operant conditioning facilitates learned associations between behaviours and outcomes, biasing future action selection to maximise reward and avoid punishment. To elucidate the underlying neural mechanisms, we built a high-throughput tracker for Drosophila melanogaster , combining real-time behaviour detection with closed-l...
Preprint
Deviations from Brownian motion leading to anomalous diffusion are ubiquitously found in transport dynamics, playing a crucial role in phenomena from quantum physics to life sciences. The detection and characterization of anomalous diffusion from the measurement of an individual trajectory are challenging tasks, which traditionally rely on calculat...
Article
Full-text available
Neural stem cell (NSC) populations persist in the adult vertebrate brain over a lifetime, and their homeostasis is controlled at the population level through unknown mechanisms. Here, we combine dynamic imaging of entire NSC populations in their in vivo niche over several weeks with pharmacological manipulations, mathematical modeling, and spatial...
Preprint
Single particle tracking allows probing how biomolecules interact physically with their natural environments. A fundamental challenge when analysing recorded single particle trajectories is the inverse problem of inferring the physical model or class of models of the underlying random walks. Reliable inference is made difficult by the inherent stoc...
Article
Full-text available
Oncoplastic surgery allows an increase in the number of indications for conservative breast cancer treatments. However, uncertainty as to whether it can be performed still exists in certain situations such as with multicentric or multifocal lesions, even when the breast volume can accommodate it. With the aid of a virtual reality software, DIVA, al...
Article
Full-text available
Background Ischiopagus us twins share parts of the spine, central nervous system, gastrointestinal and genitourinary tracts with various degrees of severity. Their separation is a surgical challenge. From the perspective of the plastic surgeon, one of the straightforward technical problems of conjoined twin separation is the coverage of the large r...
Article
Full-text available
Experimentally recorded point cloud data, such as those generated by single-molecule localization microscopy, are continuously increasing in size and dimension. Gaining an intuitive understanding and facilitating the analysis of such multidimensional data remains challenging. Here we report a new open-source software platform, Genuage, that enables...
Article
Craniofacial fractures management is challenging to teach due to the complex anatomy of the head, even when using three-dimensional CT-scan images. DIVA is a software allowing the straightforward visualization of CT-scans in a user-friendly three-dimensional virtual reality environment. Here, we assess DIVA as an educational tool for craniofacial t...
Preprint
Neural stem cell (NSC) populations persist in the adult vertebrate brain over a life time, and their homeostasis is controlled at the population level. The nature and properties of these coordination mechanisms remain unknown. Here we combine dynamic imaging of entire NSC populations in their in vivo niche over weeks, pharmacological manipulations,...
Article
As three-dimensional microscopy becomes commonplace in biological re- search, there is an increasing need for researchers to be able to view experi- mental image stacks in a natural three-dimensional viewing context. Through stereoscopy and motion tracking, commercial virtual reality headsets provide a solution to this important visualization chall...
Preprint
Full-text available
As three-dimensional microscopy becomes commonplace in biological research, there is an increasing need for researchers to be able to view experimental image stacks in a natural three-dimensional viewing context. Through stereoscopy and motion tracking, commercial virtual reality headsets provide a solution to this important visualization challenge...
Preprint
Full-text available
The quantity of experimentally recorded point cloud data, such generated in single-molecule experiments, is increasing continuously in both size and dimension. Gaining an intuitive understanding of the data and facilitating multi-dimensional data analysis remains a challenge. It is especially challenging when static distribution properties are not...
Article
Full-text available
We devise a method to detect and estimate forces in a heterogeneous environment based on experimentally recorded stochastic trajectories. In particular, we focus on systems modeled by the heterogeneous overdamped Langevin equation. Here, the observed drift includes a "spurious” force term when the diffusivity varies in space. We show how Bayesian i...
Article
Full-text available
Nervous systems have the ability to select appropriate actions and action sequences in response to sensory cues. The circuit mechanisms by which nervous systems achieve choice, stability and transitions between behaviors are still incompletely understood. To identify neurons and brain areas involved in controlling these processes, we combined a lar...
Article
We present a Bayesian framework for inferring spatio-temporal maps of diffusivity and potential fields from recorded trajectories of single molecules inside living cells. The framework naturally lets us regularise the high-dimensional inference problem using prior distributions in order to obtain robust results. To overcome the computational comple...
Preprint
Full-text available
Molecular profiles of neurons influence information processing, but bridging the gap between genes, circuits and behavior has been very difficult. Furthermore, the behavioral state of an animal continuously changes across development and as a result of sensory experience. How behavioral state influences molecular cell state is poorly understood. He...
Preprint
Full-text available
We devise a method to obtain a robust estimate of forces in a heterogeneous environment based on experimentally recorded trajectories. In particular, we focus on systems modeled by the heterogeneous overdamped Langevin equation. Here, the observed force includes a "spurious" force term due to heterogeneous diffusivity. We show how Bayesian inferenc...
Article
Full-text available
Abstract Monitoring virus assembly at the nanoscale in host cells remains a major challenge. Human immunodeficiency virus type 1 (HIV-1) components are addressed to the plasma membrane where they assemble to form spherical particles of 100 nm in diameter. Interestingly, HIV-1 Gag protein expression alone is sufficient to produce virus-like particle...
Poster
Full-text available
A marginalized Bayesian method to address uncertainty in the stochastic integration convention in the overdamped Langevin equation for biological data analysis applications.
Preprint
Full-text available
Monitoring virus assembly dynamic at the nanoscale level in host cells remains a major challenge. Human Immunodeficiency Virus type 1 (HIV-1) components are addressed to the plasma membrane where they assemble to form spherical particles of 100nm in diameter. HIV-1 Gag protein expression alone is sufficient to produce virus-like particles (VLPs) th...
Article
Full-text available
Long-distance olfactory search behaviors depend on odor detection dynamics. Due to turbulence, olfactory signals travel as bursts of variable concentration and spacing and are characterized by long-tail distributions of odor/no-odor events, challenging the computing capacities of olfactory systems. How animals encode complex olfactory scenes to tra...
Data
Raster plot of pseudo-populations of ORNs (A) and PNs (B) in response to the same frozen sequence of white-noise odor stimuli (correlation time 50 ms). Successive lines with the same color correspond to the repetition of the stimulation sequence in the same neuron. Below each raster, the population peri-stimulus time histogram is included. (EPS)
Data
Parametrization of the shapes of PN linear filter sets. Short term linear filters of 97 PNs were time-shifted according to their onset times and the PC analysis was performed again. (A) Time-shifted linear filters sorted by decreasing θ (see Fig 4A). (B) First two principal components for the PN short-term filter set. Same conventions as in Fig 4D....
Data
Comparison of whole antenna and peri-sensillum odor delivery devices. (A) Number of action potentials evoked until the firing frequency returned to baseline in response to 200-ms stimuli with different pheromone loads (n = 7). The 10 ng pheromone load used with the whole antenna stimulator induced approximatively the same ORN responses as 1 to 10 p...
Preprint
Full-text available
Nervous systems across the animal kingdom have the ability to select appropriate actions and sequences of actions in response to sensory cues. The circuit mechanisms by which nervous systems achieve choice, stability and transitions between behaviors are still incompletely understood. To identify neurons and brain areas involved in controlling thes...
Article
Full-text available
Rac1 is a small RhoGTPase switch that orchestrates actin branching in space and time and protrusion/retraction cycles of the lamellipodia at the cell front during mesenchymal migration. Biosensor imaging has revealed a graded concentration of active GTP-loaded Rac1 in protruding regions of the cell. Here, using single-molecule imaging and super-res...
Preprint
Long-distance olfactory search behaviors depend on odor detection dynamics. Due to turbulence, olfactory signals travel as bursts of variable concentration and spacing and are characterized by long-tail distributions of odor/no-odor events, challenging the computing capacities of olfactory systems. How animals encode complex olfactory scenes to tra...
Preprint
The dynamics of the cytoskeleton and cell shape relies on the coordinated activation of RhoGTPase molecular switches. Among them, Rac1 participates to the orchestration in space and time of actin branching and protrusion/retraction cycles of the lamellipodia at the cell front during mesenchymal migration. Biosensor imaging has revealed a graded con...
Article
Even a simple sensory stimulus can elicit distinct innate behaviors and sequences. During sensorimotor decisions, competitive interactions among neurons that promote distinct behaviors must ensure the selection and maintenance of one behavior, while suppressing others. The circuit implementation of these competitive interactions is still an open qu...
Article
Even a simple sensory stimulus can elicit distinct innate behaviors and sequences. During sensorimotor decisions, competitive interactions among neurons that promote distinct behaviors must ensure the selection and maintenance of one behavior, while suppressing others. The circuit implementation of these competitive interactions is still an open qu...
Article
Voltage-gated sodium (Na$_v$) channels are responsible for the depolarizing phase of the action potential in most nerve cells and Na$_v$ channel localization to the axon initial segment is vital to action potential initiation. Na$_v$ channels in the soma play a role in the transfer of axonal output information to the rest of the neuron and in synap...
Article
Tracking single molecules in living cells provides invaluable information on their environment and on the interactions that underlie their motion. New experimental techniques now permit the recording of large amounts of individual trajectories, enabling the implementation of advanced statistical tools for data analysis. In this primer, we present a...
Article
Full-text available
Genome editing with a Cas9 scalpel The Cas9 nuclease forms the heart of the CRISPR-Cas genome editing system. Cas9 binds small guide RNAs that direct it to its target sites, where the nuclease either cleaves or binds to genomic DNA. Knight et al. used single-molecule imaging to track Cas9 in living cells. Cas9 searches the genome for its target sit...
Article
Full-text available
In this paper, we consider the problem of searching for a source that releases particles in a turbulent medium with searchers having binary sensors and limited space perception.To this aim, we extend an information-theoric strategy to multiple searchers and demonstrate its efficiency both in simulation and robotic experiments. The search time is fo...
Article
Single-particle tracking (SPT) grants unprecedented insight into cellular function at the molecular scale [1]. Throughout the cell, the movement of single-molecules is generally heterogeneous and complex. Hence, there is an imperative to understand the multi-scale nature of single-molecule dynamics in biological systems. We have previously shown th...
Article
Full-text available
In recent years Bayesian Inference has become an efficient tool to analyse single molecule trajectories. Recently, high density single molecule tagging, Langevin Equation modelling and Bayesian Inference [10] have been used to infer diffusion, force and potential fields at the full cell scale. In this short comment, we point out pitfalls [1, 2] to...
Article
The scaffold protein gephyrin plays a critical regulatory role in the transmission of nerve signals in inhibitory synapses.. Its interactions with receptors of inhibitory neurotransmitters, such as glycine or GABA, are postulated to be a key molecular mechanism of synaptic formation and plasticity. Previous studies have shown that glycine receptors...
Conference Paper
We present a new method for calibrating an optical-tweezer setup that is based on Bayesian inference¹. This method employs an algorithm previously used to analyze the confined trajectories of receptors within lipid rafts2,3. The main advantages of this method are that it does not require input parameters and is insensitive to systematic errors like...
Article
Full-text available
Robots designed to track chemical leaks in hazardous industrial facilities1 or explosive traces in landmine fields2 face the same problem as insects foraging for food or searching for mates3: the olfactory search is constrained by the physics of turbulent transport4. The concentration landscape of wind borne odors is discontinuous and consists of s...
Article
There are many differences between what can be extracted from biomolecules motion using small numbers of long trajectories (Qdots, Nanoparticles, fluorophores) or large numbers of short, dense trajectories (PALM, uPaint, Storm). Long time recordings allow various estimators to converge towards mostly accurate values, but don't allow access to the s...
Article
Protein mobility is conventionally analyzed in terms of an effective diffusion. Yet, this description often fails to properly distinguish and evaluate the physical parameters (such as the membrane friction) and the biochemical interactions governing the motion. Here, we present a method combining high-density single-molecule imaging and statistical...
Article
Full-text available
Membrane proteins move in heterogeneous environments with spatially (sometimes temporally) varying friction and with biochemical interactions with various partners. It is important to reliably distinguish different modes of motion to improve our knowledge of the membrane architecture and to understand the nature of interactions between membrane pro...
Article
Full-text available
We present a new method for calibrating an optical-tweezer setup that does not depend on input parameters and is less affected by systematic errors like drift of the setup. It is based on an inference approach that uses Bayesian probability to infer the diffusion coefficient and the potential felt by a bead trapped in an optical or magnetic trap. I...
Article
Full-text available
Various insects and small animals can navigate in turbulent streams to find their mates (or food) from sparse pheromone (odor) detections. Their access to internal space perception and use of cognitive maps still are heavily debated, but for some of them, limited space perception seems to be the rule. However, this poor space perception does not pr...