Protocol for the enhanced analysis of electrophysiological data from high-density multi-electrode arrays with nicespike and spikeNburst

High-density multi-electrode arrays enable the recording of in vitro neuronal activity with exceptional spatial and temporal resolution. Here, we describe a protocol for analyzing these extensive datasets by using two complementary tools. The nicespike tool implements a full electrophysiological data analysis pipeline featuring graphics processing unit-accelerated spike sorting via template matching with Kilosort, enabling accurate identification of neuronal units across multiple electrodes. The spikeNburst tool incorporates advanced techniques for spike train filtering, burst and network burst detection, and synchronization analysis.