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Robustness of spike deconvolution for neuronal calcium imaging

Pachitariu, M; Stringer, C; Harris, KD; (2018) Robustness of spike deconvolution for neuronal calcium imaging. Journal of Neuroscience , 38 (37) pp. 7976-7985. 10.1523/JNEUROSCI.3339-17.2018. Green open access

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Abstract

Calcium imaging is a powerful method to record the activity of neural populations in many species, 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 on out-of-sample test data. 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 from the visual cortex of mice of either sex. 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.

Type: Article
Title: Robustness of spike deconvolution for neuronal calcium imaging
Open access status: An open access version is available from UCL Discovery
DOI: 10.1523/JNEUROSCI.3339-17.2018
Publisher version: https://doi.org/10.1523/JNEUROSCI.3339-17.2018
Language: English
Additional information: This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/ licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.
Keywords: calcium imaging, spike deconvolution, spike inference
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology > Department of Neuromuscular Diseases
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
URI: https://discovery.ucl.ac.uk/id/eprint/10055771
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