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AutoClean EEG w/ Pylossless

What is Autoclean EEG?

Autoclean EEG is a Part 11 capable fully automated pipeline for EEG preprocessing and analysis. Core preprocessing functions are performed by Pylossless. Autoclean EEG adds robust QI reporting, database logging, file/metadata management, and standardized analysis routines. The pipeline handles continuous and event related data and multiple EEG types including murine probe based EEG.

Special

A heartfelt thank you to the PyLossless team for their innovative EEG processing pipeline and to the MNE team for their comprehensive M/EEG analysis package. Your open-source contributions have been invaluable to this project and the broader neuroscience community.

Part 11 Compliance Features (Optional)

  • (✓) Secure electronic records management.
  • (✓) Authenticated electronic signatures.
  • (✓) Comprehensive audit trails.
  • (✓) Personnel training on system use.

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Tech Stack

Autoclean EEG leverages Python for core pipeline development, ensuring compatibility with a broad range of signal processing tools. It supports common EEG file formats (EEGLAB .set, BIDS) and outputs results in JSON and PDF reports. Data is managed using a NoSQL document database, with integration to REDCap via serverless functions. Minimal dependencies are ensured through modern Python packaging by using uv.

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Key Features

  • 🔄 Automated BIDS conversion
  • 🧹 Advanced preprocessing techniques
  • 🎯 Intelligent artifact rejection
  • 📊 Comprehensive quality control
  • 📝 Detailed reporting

Quick Start

# Set environment variables
export AUTOCLEAN_DIR=/path/to/output
export AUTOCLEAN_CONFIG=config.yml

# Run the pipeline
python -m autoclean_preprocessing.autoclean_pipeline_v2

Requirements

The pipeline requires Python ≥3.10 and the following key dependencies:

  • mne
  • pylossless
  • pyprep
  • autoreject
  • and more (see requirements.txt)

Documentation Structure

  • Getting Started: Installation and basic configuration
  • Pipeline: Detailed documentation of each pipeline stage
  • API Reference: Complete function and class documentation
  • Examples: Practical examples and use cases