MLE-Toolbox: An Open-Source Toolbox for Comprehensive EEG and MEG Data Analysis

TL;DR

MLE-Toolbox is a comprehensive, open-source MATLAB toolbox that streamlines the entire EEG and MEG data analysis process with automation, visualization, and interoperability features.

Contribution

It introduces an integrated GUI platform combining multiple analysis methods and automation tools for EEG/MEG data, enhancing accessibility and reproducibility.

Findings

Includes automated artifact rejection methods like ICA, SSP, SSS.

Supports multiple source localization techniques such as MNE, dSPM, sLORETA, beamforming.

Provides interoperability with major neuroimaging platforms.

Abstract

MLE-Toolbox is a comprehensive open-source MATLAB toolbox for end-to-end analysis of magnetoencephalography (MEG) and electroencephalography (EEG) data. Inspired by widely used neuroimaging platforms such as Brainstorm and FieldTrip, it integrates the full analysis pipeline within a unified and user-friendly graphical interface (GUI), covering raw data import, preprocessing, source localization, functional connectivity, oscillatory analysis, and machine learning-based classification. The toolbox includes automated artifact rejection methods, including independent component analysis (ICA), signal-space projection (SSP), and signal-space separation (SSS); multiple source localization approaches, including minimum norm estimation (MNE), dynamic statistical parametric mapping (dSPM), standardized low-resolution brain electromagnetic tomography (sLORETA), and beamforming; multi-atlas parcellation with anatomical visualization; spectral power analysis with frequency-band brain mapping; phase-amplitude coupling (PAC); graph-theoretic brain network analysis; and integrated machine learning and deep learning classifiers. MLE-Toolbox also provides native interoperability with Brainstorm, FieldTrip, EEGLAB, and FreeSurfer, allowing researchers to build on established workflows while benefiting from additional automation, interactive visualization, and one-click academic report generation. Freely available for non-commercial use, MLE-Toolbox is designed to lower the barrier to rigorous, reproducible MEG/EEG research.