title: Automated quantification of neuronal networks and single-cell calcium dynamics using calcium imaging.
abstract: 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.
  
  
  METHODS
  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.
  
  
  CONCLUSIONS
  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.
authors: Department of Bioengineering, University of Pennsylvania, United States.
authors: Tapan P
authors: TP
authors: Patel
authors: Department of Bioengineering, University of Pennsylvania, United States.
authors: Karen
authors: K
authors: Man
authors: Department of Cell Biology and Neuroscience, Rutgers University, United States.
authors: Bonnie L
authors: BL
authors: Firestein
authors: Department of Bioengineering, University of Pennsylvania, United States; Department of Neurosurgery, University of Pennsylvania, United States. Electronic address: dmeaney@seas.upenn.edu.
authors: David F
authors: DF
authors: Meaney
mesh_terms: D022126:Access to Information; D000465:Algorithms; D000818:Animals; D002118:Calcium / Q000378:metabolism*; D002478:Cells, Cultured; D006624:Hippocampus / Q000166:cytology / Q000502:physiology; D006801:Humans; D008822:Mice, Transgenic; D009154:Mutation; D019579:Neocortex / Q000166:cytology / Q000502:physiology; D009434:Neural Pathways / Q000166:cytology / Q000502:physiology; D009474:Neurons / Q000166:cytology / Q000502:physiology*; D061848:Optical Imaging / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D010507:Periodicity; D017207:Rats, Sprague-Dawley; D059010:Single-Cell Analysis / Q000379:methods*; D012984:Software; D058067:Wavelet Analysis; D016875:tau Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: C054369:MAPT protein, human; D016875:tau Proteins; D002118:Calcium
keywords: Calcium imaging; Event detection; FluoroSNNAP; Functional connectivity; Neuronal phenotype; Synchrony
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