المؤلفون: Yger, Pierre, Spampinato, Giulia Lb, Esposito, Elric, Lefebvre, Baptiste, Deny, Stéphane, Gardella, Christophe, Stimberg, Marcel, Jetter, Florian, Zeck, Guenther, Picaud, Serge, Duebel, Jens, Marre, Olivier

المساهمون: Institut de la Vision, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Statistique de l'ENS (LPS), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), École normale supérieure - Paris (ENS-PSL), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Natural and Medical Sciences Institute Reutlingen (NMI), ANR-10-LABX-0065,LIFESENSES,DES SENS POUR TOUTE LA VIE(2010), ANR-14-CE13-0003,AXODE,Inactivation des canaux sodium axonaux: implications pour l'excitabilité et la transmission synaptique(2014)

المصدر: EISSN: 2050-084X ; eLife ; https://hal.sorbonne-universite.fr/hal-01774438Test ; eLife, 2018, 7, pp.e34518. ⟨10.7554/eLife.34518⟩

مصطلحات موضوعية: electrophysiology, mouse, neural ensemble, neuroscience, population recording, rat, silicon probe, spike sorting, [PHYS]Physics [physics], [SDV]Life Sciences [q-bio]

الوصف: International audience ; In recent years, multielectrode arrays and large silicon probes have been developed to record simultaneously between hundreds and thousands of electrodes packed with a high density. However, they require novel methods to extract the spiking activity of large ensembles of neurons. Here, we developed a new toolbox to sort spikes from these large-scale extracellular data. To validate our method, we performed simultaneous extracellular and loose patch recordings in rodents to obtain 'ground truth' data, where the solution to this sorting problem is known for one cell. The performance of our algorithm was always close to the best expected performance, over a broad range of signal-to-noise ratios, in vitro and in vivo. The algorithm is entirely parallelized and has been successfully tested on recordings with up to 4225 electrodes. Our toolbox thus offers a generic solution to sort accurately spikes for up to thousands of electrodes.

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/29557782; hal-01774438; https://hal.sorbonne-universite.fr/hal-01774438Test; https://hal.sorbonne-universite.fr/hal-01774438/documentTest; https://hal.sorbonne-universite.fr/hal-01774438/file/elife-34518-v2.pdfTest; PUBMED: 29557782; PUBMEDCENTRAL: PMC5897014

الإتاحة: https://doi.org/10.7554/eLife.34518Test
https://hal.sorbonne-universite.fr/hal-01774438Test
https://hal.sorbonne-universite.fr/hal-01774438/documentTest
https://hal.sorbonne-universite.fr/hal-01774438/file/elife-34518-v2.pdfTest

المؤلفون: Lefebvre, Baptiste, Yger, Pierre, Marre, Olivier

المساهمون: Laboratoire de Physique Statistique de l'ENS (LPS), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), École normale supérieure - Paris (ENS-PSL), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut de la Vision, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

المصدر: ISSN: 0928-4257 ; Journal of Physiology - Paris ; https://hal.sorbonne-universite.fr/hal-01484086Test ; Journal of Physiology - Paris, 2017, ⟨10.1016/j.jphysparis.2017.02.005⟩.

مصطلحات موضوعية: Electrophysiology, Signal processing, Spike sorting, Template matching, Multi electrode array, Micro electrode array, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO]

الوصف: International audience ; In recent years, arrays of extracellular electrodes have been developed and manufactured to record simultaneously from hundreds of electrodes packed with a high density. These recordings should allow neuroscientists to reconstruct the individual activity of the neurons spiking in the vicinity of these electrodes, with the help of signal processing algorithms. Algorithms need to solve a source separation problem, also known as spike sorting. However, these new devices challenge the classical way to do spike sorting. Here we review different methods that have been developed to sort spikes from these large-scale recordings. We describe the common properties of these algorithms, as well as their main differences. Finally, we outline the issues that remain to be solved by future spike sorting algorithms.

العلاقة: hal-01484086; https://hal.sorbonne-universite.fr/hal-01484086Test; https://hal.sorbonne-universite.fr/hal-01484086/documentTest; https://hal.sorbonne-universite.fr/hal-01484086/file/Lefebvre_Recent_progress_in.pdfTest

الإتاحة: https://doi.org/10.1016/j.jphysparis.2017.02.005Test
https://hal.sorbonne-universite.fr/hal-01484086Test
https://hal.sorbonne-universite.fr/hal-01484086/documentTest
https://hal.sorbonne-universite.fr/hal-01484086/file/Lefebvre_Recent_progress_in.pdfTest

المؤلفون: Botella-Soler, Vicente, Deny, Stéphane, Martius, Georg, Marre, Olivier, Tkačik, Gašper

المساهمون: Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), Institut de la Vision, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Max-Planck-Institut für Intelligente Systeme, Max-Planck-Gesellschaft, HAL UPMC, Gestionnaire, Institute of Science and Technology [Austria] (IST Austria), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)

المصدر: PLoS Computational Biology
PLoS Computational Biology, 2018, 14 (5), pp.e1006057. ⟨10.1371/journal.pcbi.1006057⟩
PLoS Computational Biology, Public Library of Science, 2018, 14 (5), pp.e1006057. ⟨10.1371/journal.pcbi.1006057⟩
PLoS Computational Biology, Vol 14, Iss 5, p e1006057 (2018)

مصطلحات موضوعية: Retinal Ganglion Cells, Male, Computer and Information Sciences, Visible Light, Ganglion Cells, Light, Neural Networks, QH301-705.5, Physiology, Ocular Anatomy, Models, Neurological, Action Potentials, Neurophysiology, Membrane Potential, Retina, Animal Cells, Ocular System, Medicine and Health Sciences, Signal Decoders, Animals, Rats, Long-Evans, Biology (General), [SDV.MHEP.OS]Life Sciences [q-bio]/Human health and pathology/Sensory Organs, Neurons, Quantitative Biology::Neurons and Cognition, Physics, Electromagnetic Radiation, Biology and Life Sciences, Afferent Neurons, Computational Biology, Cell Biology, Rats, Electrophysiology, Luminance, Nonlinear Dynamics, [SDV.MHEP.OS] Life Sciences [q-bio]/Human health and pathology/Sensory Organs, Cellular Neuroscience, Physical Sciences, Engineering and Technology, Neural Networks, Computer, Cellular Types, Anatomy, Electronics, Research Article, Neuroscience

الوصف: Retina is a paradigmatic system for studying sensory encoding: the transformation of light into spiking activity of ganglion cells. The inverse problem, where stimulus is reconstructed from spikes, has received less attention, especially for complex stimuli that should be reconstructed “pixel-by-pixel”. We recorded around a hundred neurons from a dense patch in a rat retina and decoded movies of multiple small randomly-moving discs. We constructed nonlinear (kernelized and neural network) decoders that improved significantly over linear results. An important contribution to this was the ability of nonlinear decoders to reliably separate between neural responses driven by locally fluctuating light signals, and responses at locally constant light driven by spontaneous-like activity. This improvement crucially depended on the precise, non-Poisson temporal structure of individual spike trains, which originated in the spike-history dependence of neural responses. We propose a general principle by which downstream circuitry could discriminate between spontaneous and stimulus-driven activity based solely on higher-order statistical structure in the incoming spike trains.
Author summary Neurons in the retina transform patterns of incoming light into sequences of neural spikes. We recorded from ∼100 neurons in the rat retina while it was stimulated with a complex movie. Using machine learning regression methods, we fit decoders to reconstruct the movie shown from the retinal output. We demonstrated that retinal code can only be read out with a low error if decoders make use of correlations between successive spikes emitted by individual neurons. These correlations can be used to ignore spontaneous spiking that would, otherwise, cause even the best linear decoders to “hallucinate” nonexistent stimuli. This work represents the first high resolution single-trial full movie reconstruction and suggests a new paradigm for separating spontaneous from stimulus-driven neural activity.

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=pmid_dedup__::629fed72dfb9c03352e3a32cd3dd0ad9Test
http://europepmc.org/articles/PMC5944913Test

المؤلفون: Prentice, Jason S., Loback, Adrianna R., Ioffe, Mark L., IIBerry, Michael J., Marre, Olivier, Tkačik, Gašper

المصدر: PLoS Computational Biology; 11/17/2016, Vol. 12 Issue 11, p1-34, 34p, 11 Graphs

مصطلحات موضوعية: RETINAL ganglion cells, NERVOUS system, ERROR detection (Information theory), ERRORS-in-variables models, CODING theory

مستخلص: Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina. [ABSTRACT FROM AUTHOR]

: Copyright of PLoS Computational Biology is the property of Public Library of Science and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

المؤلفون: Lefebvre, Baptiste^1,2 baptiste.lefebvre@ens.fr, Yger, Pierre¹, Marre, Olivier¹

المصدر: Journal of Physiology (09284257). Nov2016 Part A, Vol. 110 Issue 4, p327-335. 9p.

مصطلحات موضوعية: *ACTION potentials, *ELECTRODES, *COMPUTER algorithms, *NEUROSCIENTISTS, *SIGNAL separation

مستخلص: In recent years, arrays of extracellular electrodes have been developed and manufactured to record simultaneously from hundreds of electrodes packed with a high density. These recordings should allow neuroscientists to reconstruct the individual activity of the neurons spiking in the vicinity of these electrodes, with the help of signal processing algorithms. Algorithms need to solve a source separation problem, also known as spike sorting. However, these new devices challenge the classical way to do spike sorting. Here we review different methods that have been developed to sort spikes from these large-scale recordings. We describe the common properties of these algorithms, as well as their main differences. Finally, we outline the issues that remain to be solved by future spike sorting algorithms. [ABSTRACT FROM AUTHOR]

المؤلفون: Lefebvre, Baptiste

المساهمون: Université Paris sciences et lettres, Mora, Thierry, Marre, Olivier

مصطلحات موضوعية: Neurosciences computationnelles, Électrophysiologie, Tri de potentiels d'action, Rétine, Extraction de caractéristique, Dépendance au context, Computational neuroscience, Electrophysiology, Spike sorting, Retina, Feature extraction, Context dependency, 616.8

الوصف: Les neurones sont les unités de calcul fondamentales du système nerveux central. De récentes avancées technologiques permettent d'enregistrer simultanément l'activité de milliers de cellules. Le développement de réseaux de microélectrodes qui possèdent des milliers d’électrodes groupées densément en est un exemple typique. Il renouvelle le défi du tri des potentiels d’actions des signaux enregistrés. Je passe d'abord en revue les problèmes associés aux méthodes de tri, et je compare les algorithmes qui ont été proposés. Je présente ensuite un nouvel algorithme permettant de trier les potentiels d’action en ligne pour des enregistrements à grande échelle. Le partitionnement en ligne basé sur la densité et l'appariement de motifs sont essentiels pour obtenir de bonnes performances. Le logiciel a été validé sur des enregistrements synthétiques et des données réelles de vérification. Finalement, je présente une application spécifique sur la rétine où le tri des potentiels d’action en ligne pourrait être utile. Classiquement, les cellules ganglionnaires, la sortie de la rétine, sont supposées extraire des caractéristiques spécifiques de la scène visuelle telles que des augmentations ou des diminutions de luminance (cellules ON ou OFF). Cependant, le traitement de la rétine dépend du contexte visuel. En utilisant une nouvelle approche perturbative, je montre que la même cellule peut être alternativement ON ou OFF en fonction du contexte naturel. Je montre qu'un modèle de réseau neuronal convolutif ajusté aux données peut récapituler cette dépendance au contexte. Les perturbations en ligne sont donc un outil prometteur pour sonder les calculs neuronaux des systèmes sensoriels. ; Neurons are the fundamental computing units of the central nervous system. Recent technological advances have made it possible to simultaneously record the activity of thousands of cells. A typical example is the development of microelectrode arrays with thousands of electrodes packed with a high density. A renewed challenge is to spike sort ...

العلاقة: http://www.theses.fr/2020UPSLE020/documentTest

الإتاحة: http://www.theses.fr/2020UPSLE020/documentTest

المؤلفون: Spampinato, Giulia Lia Beatrice

المساهمون: Sorbonne université, Marre, Olivier

مصطلحات موضوعية: Circuits, Rétine, Optogénétique, Électrophysiologie, Imagerie, Holographie digitale, Optique, Cellules bipolaires, Retina, Optogenetic, Electrophysiology, Imaging, Digital holography, Optical, Bipolar cells, 617.7

الوصف: Dans la rétine, les photorécepteurs convertissent la lumière en courants électriques qui sont transmis aux cellules bipolaires avant d'atteindre les cellules ganglionnaires (RGC), qui envoient leurs potentiels d’action au cerveau. Chaque RGC est sensible à la stimulation d’un emplacement spécifique du champ visuel, son champ récepteur. Différents types de RGCs codent différentes caractéristiques de la scène visuelle. Dans ce travail, nous cherchons à comprendre le rôle d’un type spécifique de cellules bipolaires: les cellules bipolaires à bâtonnets (RBC). Nous étudions leur rôle dans les calculs effectués par les RGCs. Nous nous concentrons sur deux populations de RGCs: les cellules sélectives à la direction, qui codent le mouvement visuel, et les RGC s OFF alpha, qui ont un champ récepteur antagoniste en centre-pourtour. Je présente une nouvelle méthode pour disséquer le circuit rétinien, qui combine une activation optique très précise des RBCs avec un enregistrement efficace des RGCs. Afin de manipuler les RBCs, j'exprime une protéine optogénétique sélectivement dans ces cellules. J'ai pu stimuler sélectivement les RBCs tout en enregistrant l'impact de cette stimulation sur les RGCs. J'ai trouvé que les RGC sélectives à la direction recevaient une entrée asymétrique des RBCs, et que les RBCs activent les réponses lointaines dans les RGCs OFF alpha, probablement parce qu’elles sont impliquées dans la formation du pourtour du champ récepteur. Ces résultats suggèrent que les RBCs sont un élément clé de deux calculs canoniques de la rétine. Plus généralement, il montre qu’une dissection précise des circuits neuronaux est cruciale pour comprendre leur fonction. ; In the retina, photoreceptors transduce light into electrical currents that are transmitted to bipolar cells before reaching ganglion cells, which send their spike trains to the brain. Each ganglion cell is sensitive to the stimulation of specific location of the visual field, its receptive field. Different types of ganglion cells (RGC) encode different ...

العلاقة: http://www.theses.fr/2018SORUS543/documentTest

الإتاحة: http://www.theses.fr/2018SORUS543/documentTest