MEASpikeR: An R package for standardized analysis and visualization of multielectrode array data

Aims Microelectrode arrays (MEA) are commonly used in neuroscience as a device for monitoring neuronal firing and synaptic activity in vitro from 2D and 3D neuronal cultures and brain slices. MEA recordings serve as powerful functional assay for neuroscience, but this is only applicable if it does not outstrip our ability to analyze the data. Here we present the MEASpikeR package, an R toolbox specifically designed for analyzing and exploring in vitro neuronal spike activity and field post synaptic potential (fPSP) recorded with the MED64 system (AlphaMED Scientific). Methods MEASpikeR consists of a set of functions in R, whose chained calls allow to define custom pipelines for processing and analyzing MEA data. An important advantage is to analyze multiple files in series and to integrate the main functions for studying neuronal firing activity (spike waveforms, spike sorting, burst analysis and network synchronization) and fPSP (input-output (IO) curve, Paired Pulse Ratio (PPR), long-term potentiation, LTP). Advanced data visualization of multiple recordings is also provided to obtain a global representation of the dynamic trends of a dataset. Results The strength of package was demonstrated by performing analysis from different datasets: recordings from 2D primary neuronal culture for a pharmacological study, recordings from brain organoids derived from iPSC-derived neurons and recordings from brain slice of mouse models of Alzheimer’s disease. Conclusions MEASpikeR toolbox provides a standardized, curative, automated analysis for efficient data processing and management of multiple MEA datasets. MEASpikeR is open-source and freely available on GitLab at https://gitlab.com/icm-institute/dac/biostats/MEASpikeR.