AutocleanEEG Pipeline is an easy-to-use command line application for automated EEG processing designed to be modular, reproducible, and audit-ready.The AutocleanEEG Pipeline is built on a foundation of MNE-Python and other opensource tools. We have also incorporated new features such as AI Vision based ICA component rejection. Our approach was inspired in part by the excellent framework implemented in PyLossless.The principal investigator has over 25+ years of signal processing experience. Our focus is on an easy to use tool with the ability to support complex, custom pipelines for advanced EEG analysis at scale.
Prerequisites:

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QuickStart

1

Install AutocleanEEG Pipeline

uv tool install autocleaneeg-pipeline
2

Run AutocleanEEG Pipeline

autocleaneeg-pipeline
AutocleanEEG CLI running
AutocleanEEG’s welcome page highlights system details, workspace setup, key commands, and provides links to documentation and the code repository.
3

View AutocleanEEG Pipeline help

autocleaneeg-pipeline help
AutocleanEEG CLI help showing available commands
AutocleanEEG’s help command displays all available commands including workspace configuration, file viewing, task management, data processing, review GUI, and authentication features.
4

View a file

autocleaneeg-pipeline view /path/to/your_file.set
AutocleanEEG viewer showing an EEG file
AutocleanEEG’s view subcommand provides a simple CLI wrapper around the excellent MNE Qt Browser project. Learn more at https://github.com/mne-tools/mne-qt-browser.