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Robustness of spike deconvolution for calcium imaging of neural spiking

View ORCID ProfileMarius Pachitariu, View ORCID ProfileCarsen Stringer, Kenneth D. Harris
doi: https://doi.org/10.1101/156786
Marius Pachitariu
1UCL Institute of Neurology, London WC1N 3BG, United Kingdom.
2UCL Department of Neuroscience, Physiology, and Pharmacology, London WC1E 6BT, United Kingdom.
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  • ORCID record for Marius Pachitariu
  • For correspondence: marius10p@gmail.com
Carsen Stringer
3Gatsby Computational Neuroscience Unit, London W1T 4JG, United Kingdom.
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Kenneth D. Harris
1UCL Institute of Neurology, London WC1N 3BG, United Kingdom.
2UCL Department of Neuroscience, Physiology, and Pharmacology, London WC1E 6BT, United Kingdom.
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Abstract

Calcium imaging is a powerful method to record the activity of neural populations, but inferring spike times from calcium signals is a challenging problem. We compared multiple approaches using multiple datasets with ground truth electrophysiology, and found that simple non-negative deconvolution (NND) outperformed all other algorithms. We introduce a novel benchmark applicable to recordings without electrophysiological ground truth, based on the correlation of responses to two stimulus repeats, and used this to show that unconstrained NND also outperformed the other algorithms when run on “zoomed out” datasets of ~10,000 cell recordings. Finally, we show that NND-based methods match the performance of a supervised method based on convolutional neural networks, while avoiding some of the biases of such methods, and at much faster running times. We therefore recommend that spikes be inferred from calcium traces using simple NND, due to its simplicity, efficiency and accuracy.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 27, 2017.
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Robustness of spike deconvolution for calcium imaging of neural spiking
Marius Pachitariu, Carsen Stringer, Kenneth D. Harris
bioRxiv 156786; doi: https://doi.org/10.1101/156786
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Robustness of spike deconvolution for calcium imaging of neural spiking
Marius Pachitariu, Carsen Stringer, Kenneth D. Harris
bioRxiv 156786; doi: https://doi.org/10.1101/156786

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