Davide Garolini1, Andreas Vitalis1, Amedeo Caflisch2. 1. Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland. 2. Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland. Electronic address: caflisch@bioc.uzh.ch.
Abstract
BACKGROUND: Modern techniques for multi-neuronal recording produce large amounts of data. There is no automatic procedure for the identification of states in recurrent voltage patterns. NEW METHOD: We propose NetSAP (Network States And Pathways), a data-driven analysis method that is able to recognize multi-neuron voltage patterns (states). To capture the subtle differences between snapshots in voltage recordings, NetSAP infers the underlying functional neural network in a time-resolved manner with a sliding window approach. Then NetSAP identifies states from a reordering of the time series of inferred networks according to a user-defined metric. The procedure for unsupervised identification of states was developed originally for the analysis of molecular dynamics simulations of proteins. RESULTS: We tested NetSAP on neural network simulations of GABAergic inhibitory interneurons. Most simulation parameters are chosen to reproduce literature observations, and we keep noise terms as control parameters to regulate the coherence of the simulated signals. NetSAP is able to identify multiple states even in the case of high internal noise and low signal coherence. We provide evidence that NetSAP is robust for networks with up to about 50% of the neurons spiking randomly. NetSAP is scalable and its code is open source. COMPARISON WITH EXISTING METHODS: NetSAP outperforms common analysis techniques, such as PCA and k-means clustering, on a simulated recording of voltage traces of 50 neurons. CONCLUSIONS: NetSAP analysis is an efficient tool to identify voltage patterns from neuronal recordings.
BACKGROUND: Modern techniques for multi-neuronal recording produce large amounts of data. There is no automatic procedure for the identification of states in recurrent voltage patterns. NEW METHOD: We propose NetSAP (Network States And Pathways), a data-driven analysis method that is able to recognize multi-neuron voltage patterns (states). To capture the subtle differences between snapshots in voltage recordings, NetSAP infers the underlying functional neural network in a time-resolved manner with a sliding window approach. Then NetSAP identifies states from a reordering of the time series of inferred networks according to a user-defined metric. The procedure for unsupervised identification of states was developed originally for the analysis of molecular dynamics simulations of proteins. RESULTS: We tested NetSAP on neural network simulations of GABAergic inhibitory interneurons. Most simulation parameters are chosen to reproduce literature observations, and we keep noise terms as control parameters to regulate the coherence of the simulated signals. NetSAP is able to identify multiple states even in the case of high internal noise and low signal coherence. We provide evidence that NetSAP is robust for networks with up to about 50% of the neurons spiking randomly. NetSAP is scalable and its code is open source. COMPARISON WITH EXISTING METHODS:NetSAP outperforms common analysis techniques, such as PCA and k-means clustering, on a simulated recording of voltage traces of 50 neurons. CONCLUSIONS:NetSAP analysis is an efficient tool to identify voltage patterns from neuronal recordings.