Ultra-fast accurate reconstruction of spiking activity from calcium imaging data

Journal of Neurophysiology
Vahid RahmatiStefan J Kiebel

Abstract

Calcium imaging provides an indirect observation of the underlying neural dynamics and enables the functional analysis of neuronal populations. However, the recorded fluorescence traces are temporally smeared, thus making the reconstruction of exact spiking activity challenging. Most of the established methods to tackle this issue are limited in dealing with issues such as the variability in the kinetics of fluorescence transients, fast processing of long-term data, high firing rates, and measurement noise. We propose a novel, heuristic reconstruction method to overcome these limitations. By using both synthetic and experimental data, we demonstrate the four main features of this method: 1) it accurately reconstructs both isolated spikes and within-burst spikes, and the spike count per fluorescence transient, from a given noisy fluorescence trace; 2) it performs the reconstruction of a trace extracted from 1,000,000 frames in less than 2 s; 3) it adapts to transients with different rise and decay kinetics or amplitudes, both within and across single neurons; and 4) it has only one key parameter, which we will show can be set in a nearly automatic way to an approximately optimal value. Furthermore, we demonstrate the ability of ...Continue Reading

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Feb 20, 2016·PLoS Computational Biology·Vahid RahmatiStefan J Kiebel

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Citations

Jul 29, 2018·Cellular and Molecular Life Sciences : CMLS·Daniel G Almeida-FilhoSidarta Ribeiro
Jun 6, 2020·Frontiers in Neural Circuits·Guillaume EtterSylvain Williams
Jul 3, 2021·Nature Communications·Murat KirtayZhao-Qi Wang

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Software Mentioned

CaBBI
UFARSA
STTC
MATLAB
BEADS
SMOOTHN
pCLAMP
VBA

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