Network Analysis Pipeline for Neuronal 2D and 3D Organoid Multielectrode Recordings

Multielectrode recordings from 2D or 3D cultures are commonly used to assess neuronal activity including action potential firing and burst rates. Yet, multielectrode recordings, which carry parallel time series, can also be used to infer functional connectivity and to compare network features from neuronal networks within neuronal 2D cultures or 3D organoids. This chapter provides a protocol for using the microelectrode array network analysis pipeline (MEA-NAP). With MEA-NAP, users with limited computational experience can easily evaluate network activity in their microelectrode array (MEA) recordings. Users with more computational experience can customize this open-source tool. Analysis of the functional connectivity and network features in MEA-NAP can provide insight into the development of neural circuits and how disruption of neuronal function, for example, in neurologic and psychiatric disorders, alters network function.