Open Access
June 2011 A Bayesian approach for inferring neuronal connectivity from calcium fluorescent imaging data
Yuriy Mishchenko, Joshua T. Vogelstein, Liam Paninski
Ann. Appl. Stat. 5(2B): 1229-1261 (June 2011). DOI: 10.1214/09-AOAS303


Deducing the structure of neural circuits is one of the central problems of modern neuroscience. Recently-introduced calcium fluorescent imaging methods permit experimentalists to observe network activity in large populations of neurons, but these techniques provide only indirect observations of neural spike trains, with limited time resolution and signal quality. In this work we present a Bayesian approach for inferring neural circuitry given this type of imaging data. We model the network activity in terms of a collection of coupled hidden Markov chains, with each chain corresponding to a single neuron in the network and the coupling between the chains reflecting the network’s connectivity matrix. We derive a Monte Carlo Expectation–Maximization algorithm for fitting the model parameters; to obtain the sufficient statistics in a computationally-efficient manner, we introduce a specialized blockwise-Gibbs algorithm for sampling from the joint activity of all observed neurons given the observed fluorescence data. We perform large-scale simulations of randomly connected neuronal networks with biophysically realistic parameters and find that the proposed methods can accurately infer the connectivity in these networks given reasonable experimental and computational constraints. In addition, the estimation accuracy may be improved significantly by incorporating prior knowledge about the sparseness of connectivity in the network, via standard L1 penalization methods.


Download Citation

Yuriy Mishchenko. Joshua T. Vogelstein. Liam Paninski. "A Bayesian approach for inferring neuronal connectivity from calcium fluorescent imaging data." Ann. Appl. Stat. 5 (2B) 1229 - 1261, June 2011.


Published: June 2011
First available in Project Euclid: 13 July 2011

zbMATH: 1223.62162
MathSciNet: MR2849773
Digital Object Identifier: 10.1214/09-AOAS303

Keywords: generalized linear model , Metropolis–Hastings , point process , sequential Monte Carlo , spike train data

Rights: Copyright © 2011 Institute of Mathematical Statistics

Vol.5 • No. 2B • June 2011
Back to Top