Accurate detection of low signal-to-noise ratio neuronal calcium transient waves using a matched filter

Agnieszka F Szymanska; Chiaki Kobayashi; Hiroaki Norimoto; Tomoe Ishikawa; Yuji Ikegaya; Zoran Nenadic

doi:10.1016/j.jneumeth.2015.10.014

Accurate detection of low signal-to-noise ratio neuronal calcium transient waves using a matched filter

J Neurosci Methods. 2016 Feb 1:259:1-12. doi: 10.1016/j.jneumeth.2015.10.014. Epub 2015 Nov 10.

Authors

Agnieszka F Szymanska¹, Chiaki Kobayashi², Hiroaki Norimoto³, Tomoe Ishikawa⁴, Yuji Ikegaya⁵, Zoran Nenadic⁶

Affiliations

¹ Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA. Electronic address: aszymans@uci.edu.
² Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. Electronic address: chi5.a1.ki6@gmail.com.
³ Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. Electronic address: hi.norimoto@gmail.com.
⁴ Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. Electronic address: tomoe0178@gmail.com.
⁵ Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Center for Information and Neural Networks, National Institute of Information and Communications Technology, Suita City, Osaka 565-0871, Japan. Electronic address: ikegaya@mol.f.u-tokyo.ac.jp.
⁶ Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA. Electronic address: znenadic@uci.edu.

PMID: 26561771
DOI: 10.1016/j.jneumeth.2015.10.014

Abstract

Background: Calcium imaging has become a fundamental modality for studying neuronal circuit dynamics both in vitro and in vivo. However, identifying calcium events (CEs) from spectral data remains laborious and difficult, especially since the signal-to-noise ratio (SNR) often falls below 2. Existing automated signal detection methods are generally applied at high SNRs, leaving a large need for an automated algorithm that can accurately extract CEs from fluorescence intensity data of SNR 2 and below.

New method: In this work we develop a Matched filter for Multi-unit Calcium Event (MMiCE) detection to extract CEs from fluorescence intensity traces of simulated and experimentally recorded neuronal calcium imaging data.

Results: MMiCE reached perfect performance on simulated data with SNR ≥ 2 and a true positive (TP) rate of 98.27% (± 1.38% with a 95% confidence interval), and a false positive(FP) rate of 6.59% (± 2.56%) on simulated data with SNR 0.2. On real data, verified by patch-clamp recording, MMiCE performed with a TP rate of 100.00% (± 0.00) and a FP rate of 2.04% (± 4.10).

Comparison with existing method(s): This high level of performance exceeds existing methods at SNRs as low as 0.2, which are well below those used in previous studies (SNR ≃ 5-10).

Conclusion: Overall, the MMiCE detector performed exceptionally well on both simulated data, and experimentally recorded neuronal calcium imaging data. The MMiCE detector is accurate, reliable, well suited for wide-spread use, and freely available at sites.uci.edu/aggies or from the corresponding author.

Keywords: Calcium transients; Dendritic spines; Detection; Low SNR; Matched filter; Multineuron calcium imaging; Somatic calcium fluctuations.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Calcium / metabolism*
Hippocampus / cytology*
Mice
Mice, Inbred C57BL
Neurons / cytology*
Optical Imaging / methods*
Patch-Clamp Techniques
Rats
Rats, Wistar
Signal-To-Noise Ratio*

Substances

Calcium