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An Extension of the Fri Framework for Calcium Transient Detection

Stephanie Reynolds, Caroline S. Copeland, View ORCID ProfileSimon R. Schultz, View ORCID ProfilePier Luigi Dragotti
doi: https://doi.org/10.1101/029751
Stephanie Reynolds
1Department of Electrical and Electronic Engineering, Imperial College London
3Centre for Neurotechnology, Imperial College London
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Caroline S. Copeland
2Department of Bioengineering, Imperial College London
3Centre for Neurotechnology, Imperial College London
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Simon R. Schultz
2Department of Bioengineering, Imperial College London
3Centre for Neurotechnology, Imperial College London
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Pier Luigi Dragotti
1Department of Electrical and Electronic Engineering, Imperial College London
3Centre for Neurotechnology, Imperial College London
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  • ORCID record for Pier Luigi Dragotti
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ABSTRACT

Two-photon calcium imaging of the brain allows the spatiotemporal activity of neuronal networks to be monitored at cellular resolution. In order to analyse this activity it must first be possible to detect, with high temporal resolution, spikes from the time series corresponding to single neurons. Previous work has shown that finite rate of innovation (FRI) theory can be used to reconstruct spike trains from noisy calcium imaging data. In this paper we extend the FRI framework for spike detection from calcium imaging data to encompass data generated by a larger class of calcium indicators, including the genetically encoded indicator GCaMP6s. Furthermore, we implement least squares model-order estimation and perform a noise reduction procedure (‘pre-whitening’) in order to increase the robustness of the algorithm. We demonstrate high spike detection performance on real data generated by GCaMP6s, detecting 90% of electrophysiologically-validated spikes.

Index Terms— Calcium imaging, Calcium transient detection, Finite rate of innovation, GCaMP6s

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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-NC-ND 4.0 International license.
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Posted October 23, 2015.
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An Extension of the Fri Framework for Calcium Transient Detection
Stephanie Reynolds, Caroline S. Copeland, Simon R. Schultz, Pier Luigi Dragotti
bioRxiv 029751; doi: https://doi.org/10.1101/029751
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An Extension of the Fri Framework for Calcium Transient Detection
Stephanie Reynolds, Caroline S. Copeland, Simon R. Schultz, Pier Luigi Dragotti
bioRxiv 029751; doi: https://doi.org/10.1101/029751

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