# Christophe Pouzat

Institut de Recherche Mathématique Avancée (IRMA)

CNRS UMR 7501

7, rue René Descartes

67084 Strasbourg Cedex

France

Phone: +33 3 68 85 01 38

mail: christophe.pouzat-at-math.unistra.fr

ORCID: 0000-0002-2844-8099

Cette page en français.

## News

- 2023 IHP program Random processes in the brain: From experimental data to Math and back, from February 27 to April 7. If you cannot join us in Paris, follow it from its home page (link
`LIVE!`

in the upper right of the page). - 2022-09, Advanced tools for data analysis in Neuroscience - 2022, for September 5 to 10 in Strasbourg.
- 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`

.

## Past and present

- 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).

## Research

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.

## Collaborations

- Peter Kloppenburg from Cologne University (Germany), my main "data provider".
- Antonio Galves (NeuroMat at the University of São Paulo) and Eva Löcherbach (Université Paris-1) on stochastic models for neuronal networks.
- Céline Duval (Painlevé lab., Lille University) and Éric Luçon (MAP5, Université Paris-Descartes / Université de Paris) on Hawkes process models for neural networks.

## Software

- The most recent versions of my codes can now be found on my GitHub page, GitLab page and PlmLab page.

## Publications

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…

## Pre-prints & reports

- 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 available on PlmLab. - 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)

## Talks

Recent talks:

- Cell Physics Master, Strasbourg University, September 28 2023:
*Quantitative Analysis of Fluorescence Data*. You can get the slides with the overview and the "in depth" document with all the "nasty details" using`Python`

. - What to do with extracellular recordings? A proposal. A talk given at the Eurandom's Stochastic Models in Life Science workshop on September 6 20223.
- What to do when you have to estimate a function? Nonparametric regression techniques. A lecture given at the summer school Advanced tools for data analysis in Neuroscience Aug 31 - Sept 9, 2023. An easy to read and print version of the lecture is available. The GitLab repository contains the PDF source files as well as the
`Python`

script (`regressogram.py`

in the`code`

folder) doing the analysis and the figures presented in the first part (on functional data analysis). The codes doing the job for the second part (on variance stabilization) are available in several languages: Python, R (the description is in French) and C. - Neuronal network structure inference by simulation, MoMA seminar, Dipartimento di Matematica, Sapienza, Università di Roma, May 19 2023.
- IHP first lecture on
*Stochastic modeling of neural networks*(March 20 2023). I reuse the material of my first two lectures at LASCON 2020:`sta_lecture_1.pdf`

and`sta_lecture_2.pdf`

that can be found on the dedicated`PlmLab`

repository; a "properly written" version of this material is also available from the same location in file`spike_train_analysis.pdf`

. - IHP talk Data: Where Do They Come From? How to Interpret Them? (March 17 2023).
- IHP scratch course on Basic neurobiology for mathematicians (March 1st 2023). More mathematical details can be found in Chapter 1 and Appendix 1 in the almost finished book: Probabilistic Spiking Neuronal Nets – Data, Models and Theorems.
- My course material for the Master Modeling for Neuronal and Cognitive Systems
*bootcamp*, Université Côte d'Azur, 2022, is in the`GitLab`

repository neuromod-bootcamp. - Course material for the Advanced tools for data analysis in Neuroscience - 2022 summer school in Strasbourg, September 5-10: Spike sorting: The prehistory (PDF file of introduction to spike sorting); the sorting tutorial,
*Spike Sorting the 'Do It Yourself' way*is available in PDF and HTML; the PDF and the HTML versions of the afternoon lecture,*Spike trains analysis basics*, are available as well; if you want more material on the statistical aspects of PSTH, etc, check last year course in folder`spike_trains_statics`

in my dedicated repository. - Reproducible Research: What is it? Why should we do it? How?. A talk given at Translational Medicine and Neurogenetics Department Retreat, April 26 2022, Maison du Kleebach.
- 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 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…

## Datasets

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.

## Acknowledgments

This web site was created with emacs + Org. The *css* was created by Diego Vicente.