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On the use of calcium deconvolution algorithms in practical contexts

View ORCID ProfileMathew H. Evans, Rasmus S. Petersen, View ORCID ProfileMark D. Humphries
doi: https://doi.org/10.1101/871137
Mathew H. Evans
1School of Psychology, University of Nottingham, UK
2Faculty of Biology, Medicine and Health, University of Manchester, UK
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Rasmus S. Petersen
2Faculty of Biology, Medicine and Health, University of Manchester, UK
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Mark D. Humphries
1School of Psychology, University of Nottingham, UK
2Faculty of Biology, Medicine and Health, University of Manchester, UK
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  • For correspondence: mark.humphries@nottingham.ac.uk
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Abstract

Calcium imaging is a powerful tool for capturing the simultaneous activity of large populations of neurons. Here we determine the extent to which our inferences of neural population activity, correlations, and coding depend on our choice of whether and how we deconvolve the calcium time-series into spike-driven events. To this end, we use a range of deconvolution algorithms to create nine versions of the same calcium imaging data obtained from barrel cortex during a pole-detection task. Seeking suitable values for the deconvolution algorithms’ parameters, we optimise them against ground-truth data, and find those parameters both vary by up to two orders of magnitude between neurons and are sensitive to small changes in their values. Applied to the barrel cortex data, we show that a substantial fraction of the processing methods fail to recover simple features of population activity in barrel cortex already established by electrophysiological recordings. Raw calcium time-series contain an order of magnitude more neurons tuned to features of the pole task; yet there is also qualitative disagreement between deconvolution methods on which neurons are tuned to the task. Finally, we show that raw and processed calcium time-series qualitatively disagree on the structure of correlations within the population and the dimensionality of its joint activity. Collectively, our results show that properties of neural activity, correlations, and coding inferred from calcium imaging are sensitive to the choice of if and how spike-evoked events are recovered. We suggest that quantitative results obtained from population calcium-imaging be verified across multiple processed forms of the calcium time-series.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Added full results for sensitivity analysis of third deconvolution algorithm to Figures 1 & 2. Added example of the variation of an inferred spike train across plausible parameters applied to a single neuron Clarified text throughout

Copyright 
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-NC 4.0 International license.
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Posted June 26, 2020.
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On the use of calcium deconvolution algorithms in practical contexts
Mathew H. Evans, Rasmus S. Petersen, Mark D. Humphries
bioRxiv 871137; doi: https://doi.org/10.1101/871137
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On the use of calcium deconvolution algorithms in practical contexts
Mathew H. Evans, Rasmus S. Petersen, Mark D. Humphries
bioRxiv 871137; doi: https://doi.org/10.1101/871137

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