Christophe Pouzat

• 2022-02-28, Interacting Hawkes processes with multiplicative inhibition written with Céline Duval and Éric Luçon has been accepted by Stochastic Processes and their Applications.
• 2021-10, two papers associated with Analysis of neuronal Ca2+ handling properties by combining perforated patch clamp recordings and the added buffer approach just came out: Datasets for calcium dynamics comparison between the whole-cell and a β-escin based perforated patch configuration in brain slices from adult mice and A simple method for getting standard error on the ratiometric calcium estimator.
• 2021-06-09, a new preprint: Morgan André and Christophe Pouzat Metastability in a System of Spiking Neurons with Synaptic Plasticity is on HAL.
• 2021-05-21, a new preprint: Céline Duval, Éric Luçon, Christophe Pouzat Interacting Hawkes processes with multiplicative inhibition is on arXiv, it presents a very cool way of working with inhibition within a "proper Hawkes' framework".
• 2021-05-20 to 06-11, do not miss BIOHASARD 2021, an online conference.
• 2021-04-15, Antonio Galves, Eva Löcherbach and myself started working on a book: Probabilistic spiking neuronal nets - Neuromathematics for the computer era, approximately a third is written. Comments, suggestions, etc; are welcome.
• 2021-04-15, a revised version of Analysis of neuronal Ca2+ handling properties by combining perforated patch clamp recordings and the added buffer approach has been accepted by Cell Calcium and is now (June 2021) out.
• 2020-12-23, the revised version of the previous pre-print has been sent back to the editor. Since he suggested splitting the manuscript in three: the core part; a data paper; a method paper describing the way to obtain error bars on the ratiometric Ca estimator; we followed the recommendation. The new method part can now be found on BioRxiv: A Simple Method for Getting Standard Error on the Ratiometric Calcium Estimator. As usual, the fully documented codes (the C code was rewritten in Python in order to make it more accessible) can be found on GitLab: getting-se-on-ratiometric-ca-estimator.
• 2020-07-10, a new preprint: Simon Hess, Christophe Pouzat, Lars Paeger, Andreas Pippow, Peter Kloppenburg (2020) Analysis of neuronal Ca2+ handling properties by combining perforated patch clamp recordings and the added buffer approach on bioRxiv.
• The next broadcast of the MOOC "Reproducible Research" started last March and will be going for a year (until March 2021). Prepared with Arnaud Legrand, Konrad Hinsen and "produced" by the INRIA Learning Lab, it is available in both English and French.
• I cosigned the open letter to Mehra et al and The Lancet as well as the open letter to Mehra et al and The New England Journal of Medicine, both initiated by James Watson.

• I am currently a CNRS researcher of the Intitut de Recherche Mathématique Avancée (IRMA) of the University of Strasbourg.
• Between January 2012 and August 2020 I was a CNRS researcher of the MAP5 the Applied Maths Laboratory of the Paris-Descartes University.
• I have been for 11 years (Jan 2001 - Dec 2011) member of the Laboratory of Brain Physiology of the same University.
• I did a two years post-doc (Jan 1999 - Dec 2000) in the laboratory of Gilles Laurent at the California Institute of Technology.
• I did my PhD at the Max Planck Institute for Biophysical Chemistry under the supervision of Alain Marty (Feb 1995 - Dec 1998).

Having a background in experimental neurophysiology, I mainly work on the analysis of data produced in this field. This work can be split into three broad categories – with associated keywords linking the task to specific statistical methodologies :

• Spike sorting – dimension-reduction, clustering, classification, Gaussian mixture models, EM algorithm, MCMC. All that is now explained in a short film on YouTube.
• Spike train analysis – point process / counting process, conditional intensity estimation, nonparametric estimation, smoothing spline, goodness of fit tests, Donsker theorem.
• Calcium imaging – Poisson regression, variance stabilization, parametric / nonparametric models, image segmentation.

In every project I try to implement what is now commonly called the reproducible research paradigm – that I prefer to call the reproducible data analysis paradigm. I am not a developer of the tools making the implementation of the paradigm possible but a daily user of them.

• Peter Kloppenburg from Cologne University (Germany), my main "data provider".
• Antonio Galves (NeuroMat at the University of São Paulo) and Eva Löcherbach on stochastic models for neuronal networks.
• Patricia Reynaud-Bouret, Christine Tuleau and Frank Grammont (J. A. Dieudonné Laboratory, University of Nice Sophia-Antipolis) on the analysis of spike trains.
• Céline Duval and Éric Luçon (MAP5, Université Paris-Descartes / Université de Paris) on Hawkes process models for neural networks.

• I am a member of the "guiding committee" of the Multi-electrodes Research Group.
• I am a member of the organizing committee of the Semin-R, a Parisian R users' group.

• Software I use: I could not work without Arch or Manjaro Linux, emacs + Org + babel, Python, R, maxima, SBCL, conkeror, TeX Live.
• Software I develop:
  • My current "experimental" efforts on spike sorting can be found and downloaded from my PouzatDetorakisEuroScipy2014 on GitHub or zenodo (doi: 10.5281/zenodo.15070) and my Neuronal-spike-sorting github as well as my Spike sorting pages. For a software implementing these ideas with an impressive user interface, look at Samuel Garcia's tridesclous.
  • STAR (Spike Train Analysis with R) is an R package.
  • CalciOMatic an R package for fluorescence calcium measurements analysis, developed jointly with Sébastien Joucla.
  • DynClust an R package for non-parametric denoising and clustering of noisy images indexed by time, developed jointly with Tiffany Lieury and Yves Rozenholc.
  • A simulator written in C of the "Galves-Löcherbach model".
  • The most recent versions of my codes can now be found on my GitHub page, GitLab page and PlmLab page.

My five latest publications:

• Céline Duval, Éric Luçon, Christophe Pouzat (2022) Interacting Hawkes processes with multiplicative inhibition, Stochastic Processes and their Applications, 148: 180-226, DOI: 10.1016/j.spa.2022.02.008.
• Haeger Alexa, Pouzat Christophe, Luecken Volker, N’Diaye Karim, Elger Christian, Kennerknecht Ingo, Axmacher Nikolai and Dinkelacker Vera (2021) Face Processing in Developmental Prosopagnosia: Altered Neural Representations in the Fusiform Face Area. Frontiers in Behavioral Neuroscience, 15: 283, DOI: 10.3389/fnbeh.2021.744466. Supplementary material available on GitHub: haeger-et-al-face-processing-in-developmental-prosopagnosia.
• Simon Hess, Christophe Pouzat, Peter Kloppenburg (2021) A simple method for getting standard error on the ratiometric calcium estimator. MethoodsX, 8: 101548, DOI: 10.1016/j.mex.2021.101548.
• Simon Hess, Christophe Pouzat, Peter Kloppenburg (2021) Datasets for calcium dynamics comparison between the whole-cell and a β-escin based perforated patch configuration in brain slices from adult mice. Data in Brief, 39: 107494, DOI: 10.1016/j.dib.2021.107494.
• Simon Hess, Christophe Pouzat, Lars Paeger, Andreas Pippow and Peter Kloppenburg (2021) Analysis of neuronal Ca2+ handling properties by combining perforated patch clamp recordings and the added buffer approach. Cell Calcium, 97: 102411, DOI: 10.1016/j.ceca.2021.102411.

More…

• Morgan André, Christophe Pouzat (2021) Metastability in a System of Spiking Neurons with Synaptic Plasticity, hal-03281732, the associated simulation and analysis codes are available from the following GitLab repository: Metastability in a System of Spiking Neurons with Synaptic Plasticity.
• Céline Duval, Éric Luçon, Christophe Pouzat (2021) Interacting Hawkes processes with multiplicative inhibition, arXiv:2105.10597, the associated simulation codes with detailed explanations are available from the following PlmLab repository: hawkes-x-hawkes.
• Antonio Galves, Eva Löcherbach and Christophe Pouzat (2021) Probabilistic spiking neuronal nets - Neuromathematics for the computer era, roughly the first third of a book we are currently working on.
• Simon Hess, Christophe Pouzat, Peter Kloppenburg (2020) A Simple Method for Getting Standard Error on the Ratiometric Calcium Estimator on BioRxiv. This is the appendix of the previous manuscript, expanded at the request of the editor. As usual, codes, data, etc, are available on GitLab.
• Simon Hess, Christophe Pouzat, Lars Paeger, Andreas Pippow, Peter Kloppenburg (2020) Analysis of neuronal Ca2+ handling properties by combining perforated patch clamp recordings and the added buffer approach on bioRxiv; the data and code are available on zenodo as well as on GitHub.
• Antonio Galves, Eva Löcherbach, Christophe Pouzat, Errico Presutti (2019) A system of interacting neurons with short term synaptic facilitation (arXiv:1903.01270); a GitLab repository with the code (in C and Python) doing the simulations and the figures (in gnuplot) is accessible: a_system_of_interacting_neurons_with_short_term_plasticity.
• Ludmila Brochini, Pierre Hodara, Christophe Pouzat, Antonio Galves (2016) Interaction graph estimation for the first olfactory relay of an insect (arXiv:1612.05226).
• Christophe Pouzat, Antoine Chaffiol and Avner Bar-Hen (2015) Homogeneity and identity tests for unidimensional Poisson processes with an application to neurophysiological peri-stimulus time histograms (hal-01113126, version 2) and the companion documents: Supplementary Material for: Homogeneity and identity tests for unidimensional Poisson processes with an application to neurophysiological peri-stimulus time histograms–R version (hal-01224765, version 1) and Supplementary Material for: Homogeneity and identity tests for unidimensional Poisson processes with an application to neurophysiological peri-stimulus time histograms–Python version (hal-01224764, version 1).
• Christophe Pouzat and Georgios Detorakis (2015) A Prelude to SPySort: Neuronal Spike Sorting with Python (hal-01111654, version 1) this is the "supplementary material" of SPySort: Neuronal Spike Sorting with Python (arXiv:1412.6383). The org-mode source file is available both on GitHub and on zenodo (doi: 10.5281/zenodo.15070)

Recent talks:

• Spike Sorting: The Prehistory talk given at the CORTICO 2022 workshop, March 16 2022.
• Simulation-based inference for neural network structure talk given in the Neuromat 2022 webminar series on March 8 2022.
• A System of Interacting Neurons with Short Term Synaptic Facilitation talk given with Eva Löchrbach at the Workshop on Mathematical Modeling and Statistical Analysis in Neuroscience, february 2 2022. A hand-out version is available with the slides, references, details, etc.
• The material for my course at the ADVANCED TOOLS FOR DATA ANALYSIS IN NEUROSCIENCE summer school (August 30 - September 3 2021) in Strasbourg is available on the following PlmLab repository: https://plmlab.math.cnrs.fr/xtof/advanced-tools-for-data-analysis-in-neuroscience-summer-school.
• Working Memory and Metastability in a System of Spiking Neurons with Synaptic Plasticity a talk given at the BIOHASARD 2021 workshop, June 3 2021. The talk handout is also available (easier to print with extra references and comments) and the video recording of the talk is on YouTube.
• Stochastic modeling of interacting neuron's systems a joint talk with Eva Löcherbach in the Neuromat/NeuroMod webminars series, May 28 2020. A short presentation of the talk is also available.
• My Lascon VIII (2020) lectures on "Spike train analysis and modeling" are available on the PlmLab server.
• Reproducible Research: What is it? Why should we do it? How?. A talk given at the IDEEV, Gif/Orsay, November 15, 2019. Source files are available at the plmlab repository.
• Material for the ELECTROPHYSIOLOGICAL TECHNIQUES TO ASSESS EPILEPSY IN MURINE MODELS in Cali, March-April 2019.
• A course on fluorescence data analysis given at the École de l'INSERM, February 6 2018. The title is in French but most of the content is in English. More material can be found on the dedicated GitLab repository.
• Four lectures and a talk given at the Latin American School on Computational Neuroscience (LASCON), São Paulo, January 2018.

More…

The datasets used in my publications are available in HDF5 format from zenodo. You are welcome to do what you want with them–including publishing with them without having to "invite" me to sign your publication–just cite your source (the DOI are given bellow):

• Tetrode recording from the antennal lobe of a locust (Schistocerca americana) (doi: 10.5281/zenodo.14607).
• Dataset from "Matthieu Delescluse and Christophe Pouzat (2006) Efficient spike-sorting of multi-state neurons using inter-spike intervals information Journal of Neuroscience Methods 150: 16-29." (doi: 10.5281/zenodo.15228).
• Data set from Pouzat and Chaffiol (2009) Journal of Neuroscience Methods 181:119.(doi: 10.5281/zenodo.14281).
• All my postdoc extracellular recordings from the locust olfactory pathway are now available –a third of the data has been lost due to CD corruption after 14 years!– (doi: 10.5281/zenodo.21589). There are roughly 15 GB of data from 14 experiments. A detailed description of the sorting of these data set is available on GitHub.

This web site was edited with emacs + Org. The css used comes from the one of Eric Schulte.