The ERGtools2 package: A Toolset for Processing and Analysing Visual Electrophysiology Data

Abstract

AbstractPurposeTo introduce and demonstrate the functionality of ERGtools2, an open-source R package for processing and analysing of visual electrophysiology data, with a focus on data integrity, shareability and long-term preservation.MethodsA dataset comprising Electroretinogram(ERG) recordings from both eyes of C57Bl/6J mice, subjected to standard ISCEV stimuli, was used to present the functionality of ERGtools2. ERGtools2 stores and organizes all recordings, metadata, and measurement information from individual examination in a single object, maintaining raw data throughout the analysis process.ResultsA standard workflow is presented exemplifying how ERGtools2 can be used to efficiently import, preprocess and analyse ERG data. Following this workflow basic ERG measurements like a and B-wave amplitudes and visualisation of a single exam as well as group statistics are obtained. Moreover, special use cases are described, including for the handling of noisy data and the storage of data in the HDF5 format to ensure long-term preservation and accessibility. ERGtools2 also provides a graphical interface.ConclusionsERGtools2 provides a comprehensive, flexible, and device-independent solution for visual electrophysiology data analysis. Its emphasis on maintaining raw data integrity, combined with advanced processing and analysis capabilities, makes it a useful tool research and potentially also clinical applications. The open-source nature and the use of open data formats promote reproducibility and data sharing in visual neurosciences.Translational RelevanceERGtools2 allows for sophisticated preclinical and clinical visual electrophysiology analyses. This will be helpful, for instance, in the context optogenetic vision-restoring, where signal shapes and amplitudes may be substantially different from normal vision.