Combining biophysical modeling and deep learning for multielectrode array neuron localization and classification

Journal of Neurophysiology
Alessio P BuccinoGaute T Einevoll

Abstract

Neural circuits typically consist of many different types of neurons, and one faces a challenge in disentangling their individual contributions in measured neural activity. Classification of cells into inhibitory and excitatory neurons and localization of neurons on the basis of extracellular recordings are frequently employed procedures. Current approaches, however, need a lot of human intervention, which makes them slow, biased, and unreliable. In light of recent advances in deep learning techniques and exploiting the availability of neuron models with quasi-realistic three-dimensional morphology and physiological properties, we present a framework for automatized and objective classification and localization of cells based on the spatiotemporal profiles of the extracellular action potentials recorded by multielectrode arrays. We train convolutional neural networks on simulated signals from a large set of cell models and show that our framework can predict the position of neurons with high accuracy, more precisely than current state-of-the-art methods. Our method is also able to classify whether a neuron is excitatory or inhibitory with very high accuracy, substantially improving on commonly used clustering techniques. Furthe...Continue Reading

References

Oct 1, 1985·Journal of Neurophysiology·D A McCormickD A Prince
May 20, 1999·Journal of Computational Neuroscience·G R Holt, C Koch
Dec 4, 2001·Journal of Neurophysiology·N L GoldingN Spruston
Sep 21, 2004·Nature Reviews. Neuroscience·Henry MarkramCaizhi Wu
Oct 9, 2004·Progress in Biophysics and Molecular Biology·Jack WatersBert Sakmann
Nov 19, 2004·Journal of Neurophysiology·Timothy J BlancheNicholas V Swindale
Feb 9, 2005·Journal of Neuroscience Methods·Mircea I Chelaru, Mandar S Jog
Mar 8, 2005·Trends in Neurosciences·Jesse H Goldberg, Rafael Yuste
May 26, 2005·Journal of Neuroscience Methods·Zoltán SomogyváriPéter Erdi
Feb 10, 2006·Journal of Neurophysiology·Carl GoldGyörgy Buzsáki
Oct 3, 2006·Progress in Brain Research·Javier DeFelipeAlberto Muñoz
Feb 3, 2007·Journal of Computational Neuroscience·Carl GoldChristof Koch
Oct 9, 2007·Biophysical Journal·Klas H Pettersen, Gaute T Einevoll
Dec 13, 2007·Physiology·Werner Göbel, Fritjof Helmchen
Sep 26, 2008·PLoS Biology·Alan Woodruff, Rafael Yuste
Jan 24, 2009·Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society·Takashi KuboMitsuyuki Nakao
Feb 10, 2009·Frontiers in Neuroinformatics·Michael L HinesEilif Muller
May 21, 2010·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Amanda FoustDavid A McCormick
Jul 28, 2010·Journal of Neuroscience Methods·Woodrow L ShewDietmar Plenz
Sep 3, 2010·Journal of Neurophysiology·Takakuni GotoRyuta Kawashima
May 27, 2011·Journal of Neurophysiology·Ferenc MechlerQin Hu
Jun 15, 2011·Journal of Computational Neuroscience·Ferenc Mechler, Jonathan D Victor
Feb 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Adrien PeyracheAlain Destexhe
Feb 24, 2012·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Takuya SasakiYuji Ikegaya
Sep 1, 2012·The European Journal of Neuroscience·Zoltán SomogyváriPéter Erdi
Sep 3, 2013·Journal of Graduate Medical Education·Gail M Sullivan, Richard Feinn
Jan 30, 2014·Frontiers in Neuroinformatics·Henrik LindénGaute T Einevoll
Jun 24, 2014·Journal of Neuroscience Methods·Isabel Delgado Ruz, Simon R Schultz
Mar 31, 2015·Neuroinformatics·Torbjørn V NessGaute T Einevoll
May 23, 2015·Journal of Neurophysiology·Costas A AnastassiouChristof Koch
Jul 21, 2015·Nature Reviews. Neuroscience·Linda Overstreet-Wadiche, Chris J McBain
Oct 10, 2015·Cell·Henry MarkramFelix Schürmann
Oct 27, 2015·Frontiers in Neural Circuits·Srikanth RamaswamyHenry Markram
Feb 3, 2016·Scientific Reports·Marleen WelkenhuysenDries Braeken
Mar 15, 2016·Nature Neuroscience·Cyrille RossantKenneth D Harris
Jun 17, 2016·Journal of Neurophysiology·Joana P NetoAdam R Kampff
Feb 21, 2018·Nature Communications·Nathan W GouwensAnton Arkhipov

❮ Previous
Next ❯

Citations

Feb 1, 2019·Journal of Neural Engineering·Alessio Paolo BuccinoAslak Tveito
Jul 11, 2020·Neuroinformatics·Alessio Paolo Buccino, Gaute Tomas Einevoll
Jul 17, 2021·Scientific Data·Csaba HorváthRichárd Fiáth

❮ Previous
Next ❯

Methods Mentioned

BETA
feature extraction
transgenic

Software Mentioned

NEURON
NaRep
3drot
Waveform
Physrot
VISAPy
TensorFlow
NeuroPixels
SqMEA
Norot

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Alessio P BuccinoPhilipp D Hafliger
Studies in Health Technology and Informatics
Mark HughesToyotaro Suzumura
© 2022 Meta ULC. All rights reserved