Automated quantification of neuronal networks and single-cell calcium dynamics using calcium imaging

J Neurosci Methods. 2015 Mar 30;243:26-38. doi: 10.1016/j.jneumeth.2015.01.020. Epub 2015 Jan 25.


Background: Recent advances in genetically engineered calcium and membrane potential indicators provide the potential to estimate the activation dynamics of individual neurons within larger, mesoscale networks (100s-1000+neurons). However, a fully integrated automated workflow for the analysis and visualization of neural microcircuits from high speed fluorescence imaging data is lacking.

New method: Here we introduce FluoroSNNAP, Fluorescence Single Neuron and Network Analysis Package. FluoroSNNAP is an open-source, interactive software developed in MATLAB for automated quantification of numerous biologically relevant features of both the calcium dynamics of single-cells and network activity patterns. FluoroSNNAP integrates and improves upon existing tools for spike detection, synchronization analysis, and inference of functional connectivity, making it most useful to experimentalists with little or no programming knowledge.

Results: We apply FluoroSNNAP to characterize the activity patterns of neuronal microcircuits undergoing developmental maturation in vitro. Separately, we highlight the utility of single-cell analysis for phenotyping a mixed population of neurons expressing a human mutant variant of the microtubule associated protein tau and wild-type tau.

Comparison with existing method(s): We show the performance of semi-automated cell segmentation using spatiotemporal independent component analysis and significant improvement in detecting calcium transients using a template-based algorithm in comparison to peak-based or wavelet-based detection methods. Our software further enables automated analysis of microcircuits, which is an improvement over existing methods.

Conclusions: We expect the dissemination of this software will facilitate a comprehensive analysis of neuronal networks, promoting the rapid interrogation of circuits in health and disease.

Keywords: Calcium imaging; Event detection; FluoroSNNAP; Functional connectivity; Neuronal phenotype; Synchrony.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Access to Information
  • Algorithms
  • Animals
  • Calcium / metabolism*
  • Cells, Cultured
  • Hippocampus / cytology
  • Hippocampus / physiology
  • Humans
  • Mice, Transgenic
  • Mutation
  • Neocortex / cytology
  • Neocortex / physiology
  • Neural Pathways / cytology
  • Neural Pathways / physiology
  • Neurons / cytology
  • Neurons / physiology*
  • Optical Imaging / methods*
  • Pattern Recognition, Automated / methods*
  • Periodicity
  • Rats, Sprague-Dawley
  • Single-Cell Analysis / methods*
  • Software*
  • Wavelet Analysis
  • tau Proteins / genetics
  • tau Proteins / metabolism


  • MAPT protein, human
  • tau Proteins
  • Calcium