EEG-Pype: An accessible MNE-Python pipeline with graphical user interface for preprocessing and analysis of resting-state electroencephalography data

Abstract

Processing of electroencephalography (EEG) data requires multiple steps to remove noise and artifacts and select good-quality data. While powerful open-source toolboxes like MNE-Python exist, their command-line nature can pose a barrier for researchers without programming experience. Here, we present EEG-Pype, an open-source (Apache-2.0 licensed) graphical user interface application using MNE-Python functions. EEG-Pype provides an intuitive workflow tailored for preprocessing of resting-state EEG data, including frequency band filtering, independent component analysis and atlas-based beamforming for source-level analysis. The application supports several common raw EEG input file formats and guides users through a comprehensive pipeline focused on manual bad channel and epoch selection. Manual steps are streamlined using MNE-Python's interactive plots, resulting in a user-friendly experience. Configuration saving and loading allows for batch (re)runs, while a separate log is also saved, improving reproducibility and documentation. Output can be saved after filtering in canonical frequency bands, ready for further analysis. EEG-Pype includes a module for calculating quantitative EEG measures on preprocessed data, including spectral, functional connectivity and network analysis metrics. This software aims to lower the entry barrier for standardized EEG preprocessing, promoting reproducible research practices among neuroscientists and clinicians without requiring programming knowledge. EEG-Pype can be downloaded from: https://github.com/yorbenlodema/EEG-Pype and is not dependent on a specific operating system.