Community-based benchmarking improves spike rate inference from two-photon calcium imaging data.

PLoS Computational Biology
Philipp BerensMatthias Bethge

Abstract

In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators. Different algorithms for estimating spike rates from noisy calcium measurements have been proposed in the past, but it is an open question how far performance can be improved. Here, we report the results of the spikefinder challenge, launched to catalyze the development of new spike rate inference algorithms through crowd-sourcing. We present ten of the submitted algorithms which show improved performance compared to previously evaluated methods. Interestingly, the top-performing algorithms are based on a wide range of principles from deep neural networks to generative models, yet provide highly correlated estimates of the neural activity. The competition shows that benchmark challenges can drive algorithmic developments in neuroscience.

References

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
Jul 22, 2009·Biophysical Journal·Joshua T VogelsteinLiam Paninski
Jun 18, 2010·Journal of Neurophysiology·Joshua T VogelsteinLiam Paninski
Jul 23, 2013·Nature·Tsai-Wen ChenDouglas S Kim
Oct 18, 2013·Frontiers in Neural Circuits·R James CottonAndreas S Tolias
Apr 17, 2015·Current Opinion in Neurobiology·Simon PeronKarel Svoboda
May 20, 2015·Current Opinion in Neurobiology·Jeremy Freeman
Dec 15, 2015·Proceedings of the National Academy of Sciences of the United States of America·Matthias KümmererMatthias Bethge
Jan 18, 2016·Neuron·Eftychios A PnevmatikakisLiam Paninski
May 7, 2016·Neuron·Lucas TheisMatthias Bethge
Mar 16, 2017·PLoS Computational Biology·Johannes FriedrichLiam Paninski

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Citations

Apr 19, 2018·Journal of Neurophysiology·Luis O JimenezDario L Ringach
Dec 20, 2018·Journal of Neurophysiology·Marie E BelletPhilipp Berens
Feb 2, 2020·Brain Structure & Function·Christian R LeeDavid J Margolis
Feb 17, 2019·Molecular Psychiatry·Daniel DurstewitzAndreas Meyer-Lindenberg
Sep 14, 2019·Nature Reviews. Genetics·Francesca FinotelloZlatko Trajanoski
Sep 16, 2020·PLoS Computational Biology·Ziqiang WeiShaul Druckmann
Jul 13, 2018·Frontiers in Neuroscience·Peter VerstraelenWinnok H De Vos
Nov 28, 2018·ELife·Yang LiuMarkus Meister
Mar 4, 2020·Nature Methods·Kuo-Hua HuangRainer W Friedrich
Jan 11, 2020·Frontiers in Neuroscience·Jean-Marc FellousMichele Ferrante
Feb 13, 2019·Frontiers in Neural Circuits·Marcus A Triplett, Geoffrey J Goodhill
Oct 28, 2019·Nature Communications·Dario L Ringach
Oct 22, 2020·Scientific Reports·Huu HoangKeisuke Toyama
Dec 29, 2020·Journal of Neuroscience Methods·Michael Wenzel, Jordan P Hamm
Jan 26, 2021·Frontiers in Neural Circuits·Gilles VanwalleghemEthan K Scott
Mar 2, 2021·PLoS Computational Biology·Jilt SebastianMathew Magimai-Doss
Jun 5, 2021·PloS One·Weston FlemingIlana B Witten
Aug 20, 2021·Current Biology : CB·Liming TanJoshua T Trachtenberg
Jun 2, 2020·Journal of Neuroscience Methods·Jérôme TubianaGeorges Debregeas
Oct 17, 2021·Biostatistics·Yiqun T ChenDaniela M Witten

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Software Mentioned

scikit
Jupyter
R package afex
learn
lsmeans
spikefinder
GENIE

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