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SIMONE: a realistic neural network simulator to reproduce MEA-based recordings

Authors :
Isabelle E. Magnin
Christophe Pouzat
Blaise Yvert
Antoine Chaffiol
R. Escola
Régis Guillemaud
Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI)
Direction de Recherche Technologique (CEA) (DRT (CEA))
Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Laboratoire de physiologie cérébrale (LPC - UMR 8118)
Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Institut de Neurosciences cognitives et intégratives d'Aquitaine (INCIA)
Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-SFR Bordeaux Neurosciences-Centre National de la Recherche Scientifique (CNRS)
Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé (CREATIS)
Université Claude Bernard Lyon 1 (UCBL)
Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon)
Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Laboratoire d'Electronique et des Technologies de l'Information ( CEA-LETI )
Université Grenoble Alpes [Saint Martin d'Hères]-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA )
Laboratoire de physiologie cérébrale ( LPC - UMR 8118 )
Université Paris Diderot - Paris 7 ( UPD7 ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS )
Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-SFR Bordeaux Neurosciences-Centre National de la Recherche Scientifique (CNRS)
Université Jean Monnet [Saint-Étienne] (UJM)-Hospices Civils de Lyon (HCL)-Institut National des Sciences Appliquées de Lyon (INSA Lyon)
Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL)
Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Centre de Recherche et d'Application en Traitement de l'Image et du Signal (CREATIS)
Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École Supérieure Chimie Physique Électronique de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Laboratoire d'Electronique et des Technologies de l'Information (CEA-LETI)
Université Grenoble Alpes (UGA)-Direction de Recherche Technologique (CEA) (DRT (CEA))
Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)
Source :
IEEE Transactions on Neural Systems and Rehabilitation Engineering, IEEE Transactions on Neural Systems and Rehabilitation Engineering, 2008, 16 (2), pp.149-60. ⟨10.1109/TNSRE.2007.914467⟩, IEEE Transactions on Neural Systems and Rehabilitation Engineering, Institute of Electrical and Electronics Engineers, 2008, 16 (2), pp.149-60. 〈10.1109/TNSRE.2007.914467〉, IEEE Transactions on Neural Systems and Rehabilitation Engineering, Institute of Electrical and Electronics Engineers, 2008, 16 (2), pp.149-60. ⟨10.1109/TNSRE.2007.914467⟩, IEEE Transactions on Neural Systems and Rehabilitation Engineering, Institute of Electrical and Electronics Engineers, 2008, 16 (2), pp.149--160
Publication Year :
2008
Publisher :
HAL CCSD, 2008.

Abstract

International audience; Contemporary multielectrode arrays (MEAs) used to record extracellular activity from neural tissues can deliver data at rates on the order of 100 Mbps. Such rates require efficient data compression and/or preprocessing algorithms implemented on an application specific integrated circuit (ASIC) close to the MEA. We present SIMONE (Statistical sIMulation Of Neuronal networks Engine), a versatile simulation tool whose parameters can be either fixed or defined by a probability distribution. We validated our tool by simulating data recorded from the first olfactory relay of an insect. Different key aspects make this tool suitable for testing the robustness and accuracy of neural signal processing algorithms (such as the detection, alignment, and classification of spikes). For instance, most of the parameters can be defined by a probabilistic distribution, then tens of simulations may be obtained from the same scenario. This is especially useful when validating the robustness of the processing algorithm. Moreover, the number of active cells and the exact firing activity of each one of them is perfectly known, which provides an easy way to test accuracy.

Subjects

Subjects :
MESH: Microelectrodes
Computer science
MESH: Neurons
Action Potentials
Synaptic Transmission
American cockroach
law.invention
0302 clinical medicine
[INFO.INFO-TS]Computer Science [cs]/Signal and Image Processing
Application-specific integrated circuit
Relay
law
SpikeOMatic
Preprocessor
SIMONE
[ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
MESH : Algorithms
MESH: Action Potentials
Neurons
0303 health sciences
MESH : Synaptic Transmission
Artificial neural network
General Neuroscience
Rehabilitation
simulation
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
MESH : Computer Simulation
Spike sorting
[INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV]
Probability distribution
[SDV.IB]Life Sciences [q-bio]/Bioengineering
Algorithm
[SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing
Algorithms
Data compression
noise
Models, Neurological
Biomedical Engineering
extracellular
MESH: Algorithms
spike sorting
MESH : Neurons
03 medical and health sciences
MESH: Computer Simulation
Robustness (computer science)
MESH : Action Potentials
MESH: Models, Neurological
[ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM]
spike detection
[INFO.INFO-IM]Computer Science [cs]/Medical Imaging
Internal Medicine
Electronic engineering
MESH: Synaptic Transmission
MESH : Models, Neurological
Computer Simulation
integrate-and-fire
030304 developmental biology
[INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation
MESH: Nerve Net
MESH : Microelectrodes
MESH : Nerve Net
Nerve Net
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
multielectrode array (MEA)
Microelectrodes
030217 neurology & neurosurgery

Details

Language :
English
ISSN :
15344320 and 15580210
Database :
OpenAIRE
Journal :
IEEE Transactions on Neural Systems and Rehabilitation Engineering, IEEE Transactions on Neural Systems and Rehabilitation Engineering, 2008, 16 (2), pp.149-60. ⟨10.1109/TNSRE.2007.914467⟩, IEEE Transactions on Neural Systems and Rehabilitation Engineering, Institute of Electrical and Electronics Engineers, 2008, 16 (2), pp.149-60. 〈10.1109/TNSRE.2007.914467〉, IEEE Transactions on Neural Systems and Rehabilitation Engineering, Institute of Electrical and Electronics Engineers, 2008, 16 (2), pp.149-60. ⟨10.1109/TNSRE.2007.914467⟩, IEEE Transactions on Neural Systems and Rehabilitation Engineering, Institute of Electrical and Electronics Engineers, 2008, 16 (2), pp.149--160
Accession number :
edsair.doi.dedup.....21d23a18b0d2c96aea3dd799e572ff4f
Full Text :
https://doi.org/10.1109/TNSRE.2007.914467⟩