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.


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 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*


  • Calcium