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Article Dans Une Revue PLoS Computational Biology Année : 2018

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

Philipp Berens
Jeremy Freeman
  • Fonction : Auteur
Thomas Deneux
Nikolay Chenkov
  • Fonction : Auteur
Thomas Mccolgan
Artur Speiser
  • Fonction : Auteur
Marius Pachitariu
Jakob Macke
  • Fonction : Auteur
Stephan Gerhard
Srinivas Turaga
Patrick Mineault
Rainer Friedrich
Kenneth Harris
Peter Rupprecht
Johannes Friedrich
Liam Paninski
  • Fonction : Auteur
Ben Bolte
  • Fonction : Auteur
Timothy Machado
  • Fonction : Auteur
Dario Ringach
  • Fonction : Auteur
Jasmine Stone
Luke Rogerson
  • Fonction : Auteur
Nicolas Sofroniew
  • Fonction : Auteur
Jacob Reimer
  • Fonction : Auteur
Emmanouil Froudarakis
Thomas Euler
Miroslav Román Rosón
  • Fonction : Auteur
Lucas Theis
  • Fonction : Auteur
Andreas Tolias
Matthias Bethge
  • Fonction : Auteur

Résumé

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.

Dates et versions

hal-03942511 , version 1 (17-01-2023)

Identifiants

Citer

Philipp Berens, Jeremy Freeman, Thomas Deneux, Nikolay Chenkov, Thomas Mccolgan, et al.. Community-based benchmarking improves spike rate inference from two-photon calcium imaging data. PLoS Computational Biology, 2018, 14 (5), pp.e1006157. ⟨10.1371/journal.pcbi.1006157⟩. ⟨hal-03942511⟩
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