NeuroChaT: A toolbox to analyse the dynamics of neuronal encoding in freely-behaving rodents in vivo

Wellcome Open Res. 2019 Dec 9:4:196. doi: 10.12688/wellcomeopenres.15533.1. eCollection 2019.


There is a dearth of freely-available, standardised open source analysis tools available for the analysis of neuronal signals recorded in vivo in the freely-behaving animal. In response, we have developed a freely-available, open-source toolbox, NeuroChaT ( Neuron Characterisation Toolbox), specifically addressing this lacuna. Although we have particularly emphasised single unit analyses for spatial coding, NeuroChaT also characterises rhythmic properties of units and their dynamics associated with local field potential signals. NeuroChaT was developed using Python and facilitates a complete pipeline from automation of analysis to producing and managing publication-quality figures. Additionally, we have adopted a platform-independent format (Hierarchical Data Format version 5) for storing recorded and analysed data. By providing an easy-to-use software package, we aim to simplify the adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories.

Keywords: Cognitive map; data analysis; electrophysiology; open software; single unit; spatial coding.