Benchmarking Spike Rate Inference in Population Calcium Imaging

Neuron
Lucas TheisMatthias Bethge

Abstract

A fundamental challenge in calcium imaging has been to infer spike rates of neurons from the measured noisy fluorescence traces. We systematically evaluate different spike inference algorithms on a large benchmark dataset (>100,000 spikes) recorded from varying neural tissue (V1 and retina) using different calcium indicators (OGB-1 and GCaMP6). In addition, we introduce a new algorithm based on supervised learning in flexible probabilistic models and find that it performs better than other published techniques. Importantly, it outperforms other algorithms even when applied to entirely new datasets for which no simultaneously recorded data is available. Future data acquired in new experimental conditions can be used to further improve the spike prediction accuracy and generalization performance of the model. Finally, we show that comparing algorithms on artificial data is not informative about performance on real data, suggesting that benchmarking different methods with real-world datasets may greatly facilitate future algorithmic developments in neuroscience.

References

Apr 6, 1990·Science·W DenkW W Webb
Jun 5, 2003·Proceedings of the National Academy of Sciences of the United States of America·Christoph StosiekArthur Konnerth
Sep 15, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jason N D KerrFritjof Helmchen
Feb 14, 2008·Nature Reviews. Neuroscience·Jason N D Kerr, Winfried Denk
Jun 17, 2008·Nature Neuroscience·David S GreenbergJason N D Kerr
Jul 4, 2008·Journal of Neurophysiology·Takuya SasakiYuji Ikegaya
Nov 22, 2008·Pflügers Archiv : European journal of physiology·Thomas EulerWinfried Denk
Jul 22, 2009·Biophysical Journal·Joshua T VogelsteinLiam Paninski
Mar 2, 2010·Neuron·Cristopher M Niell, Michael P Stryker
Jun 18, 2010·Journal of Neurophysiology·Joshua T VogelsteinLiam Paninski
Jul 9, 2010·Journal of Neurophysiology·Ilya ValmianskiDavid Kleinfeld
Feb 25, 2011·Journal of Neurophysiology·Kevin L Briggman, Thomas Euler
Oct 5, 2012·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Jasper AkerboomLoren L Looger
May 29, 2013·Journal of Neuroscience Methods·In Jun ParkJose C Principe
Jul 19, 2013·Journal of Neural Engineering·Jon OñativiaPier Luigi Dragotti
Jul 23, 2013·Nature·Tsai-Wen ChenDouglas S Kim
Oct 18, 2013·Frontiers in Neural Circuits·R James CottonAndreas S Tolias
Nov 28, 2013·PLoS Computational Biology·Lucas TheisMatthias Bethge
Jan 9, 2014·Frontiers in Neural Circuits·Henry LütckeFritjof Helmchen
Apr 8, 2014·Neural Networks : the Official Journal of the International Neural Network Society·Ryuichi MaruyamaToru Aonishi
Apr 22, 2014·Nature Neuroscience·Emmanouil FroudarakisAndreas S Tolias
Nov 25, 2014·Nature Methods·Masatoshi InoueHaruhiko Bito
Jan 18, 2016·Neuron·Eftychios A PnevmatikakisLiam Paninski

Citations

May 22, 2016·Journal of Neuroscience Methods·Josh MerelLiam Paninski
Apr 1, 2015·PLoS Computational Biology·Dimitri YatsenkoAndreas S Tolias
May 19, 2017·Neuron·Hiroshi MakinoTakaki Komiyama
May 19, 2017·Neuron·Tsai-Wen ChenKarel Svoboda
Jun 8, 2017·PLoS Computational Biology·Sebastián A RomanoGermán Sumbre
Apr 1, 2017·Nature Methods·Weijian Yang, Rafael Yuste
Nov 2, 2017·Nature Communications·Eun Jung HwangTakaki Komiyama
Nov 14, 2017·Journal of Neural Engineering·Renaud SchuckSimon R Schultz
May 22, 2018·PLoS Computational Biology·Philipp BerensMatthias Bethge
Dec 20, 2018·Journal of Neurophysiology·Marie E BelletPhilipp Berens
Aug 30, 2016·Nature Neuroscience·Michael Z Lin, Mark J Schnitzer
Aug 30, 2016·Nature Neuroscience·Kenneth D HarrisSpencer L Smith
Jul 2, 2019·Neural Computation·David M Schwartz, O Ozan Koyluoglu
Feb 2, 2020·Brain Structure & Function·Christian R LeeDavid J Margolis
Nov 7, 2019·Science Advances·Eun Jung HwangTakaki Komiyama
Mar 13, 2020·PLoS Computational Biology·Ryohei Shibue, Fumiyasu Komaki
Sep 16, 2020·PLoS Computational Biology·Ziqiang WeiShaul Druckmann
Mar 17, 2017·Annual Review of Biophysics·Luis Carrillo-ReidRafael Yuste
Mar 16, 2017·PLoS Computational Biology·Johannes FriedrichLiam Paninski
Dec 23, 2018·Neural Computation·Christophe GardellaThierry Mora
Apr 19, 2019·International Journal of Molecular Sciences·Sudip PaudelMargaret S Saha
Nov 14, 2018·Nature Methods·Zihui ZhangMichael Häusser
Jan 18, 2019·ELife·Andrea GiovannucciEftychios A Pnevmatikakis
Feb 13, 2019·Biostatistics·Sean W JewellDaniela Witten
Dec 5, 2019·Nature Communications·Qingguang ZhangPatrick J Drew
Apr 21, 2018·Biomedical Optics Express·William J ShainJerome Mertz
Jun 27, 2020·Journal of Neural Engineering·Matthew F SinghShiNung Ching
Jul 10, 2018·Biomedical Optics Express·Li ZhuLaleh Najafizadeh
Oct 22, 2020·Scientific Reports·Huu HoangKeisuke Toyama
Sep 17, 2020·Journal of Neurophysiology·Zhengyu MaRalf Wessel
Dec 6, 2020·Pharmacology, Biochemistry, and Behavior·Alyssa G Yocky, Dan P Covey
Jan 26, 2021·Frontiers in Neural Circuits·Gilles VanwalleghemEthan K Scott
Mar 2, 2021·PLoS Computational Biology·Jilt SebastianMathew Magimai-Doss
Jan 11, 2019·The Annals of Applied Statistics·Sean Jewell, Daniela Witten

Related Concepts

Nerve Impulses
Metazoa
Calcium
Neurons
Retina
Signal Processing, Digital
Mouse, Swiss
Diagnostic Imaging
Learning
calcium indicator

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