AutoClean EEG Pipeline#

AutoClean makes EEG data processing simple and accessible for everyone - from researchers with no programming experience to advanced developers building custom analysis workflows.

🎯 For Non-Technical Users#

If you’re new to EEG processing or programming, AutoClean provides:

One-click setup: Install and configure your workspace in minutes
Web-based task builder: Create processing pipelines through an intuitive interface
Drop-and-go workflow: Simply drop your task files and run
No coding required: Process your data with simple commands

🔧 For Technical Users#

If you’re a programmer or advanced researcher, AutoClean offers:

Python integration: Full API access for custom scripts and Jupyter notebooks
Modular architecture: Build custom processing pipelines with reusable components
Advanced customization: Create sophisticated workflows with mixins and plugins
Developer tools: CLI commands and configuration management

Key Features#

Automated Preprocessing: Intelligent artifact detection and removal
Quality Control Reports: Visual summaries of processing results
User-Friendly Workspace: Organized file structure in your Documents folder
Cross-Platform: Works on Windows, Mac, and Linux
Reproducible: Consistent results across different users and systems
Extensible: Easy to add new processing methods and experimental paradigms

Why Choose AutoClean?#

Consistent Results: Eliminates variability between researchers and labs by providing standardized, validated processing workflows.

Easy to Use: Whether you’re clicking through a web interface or writing Python code, AutoClean adapts to your preferred way of working.

Research-Focused: Built by neuroscientists for neuroscientists, with features that address real research needs and workflows.

Core Concepts#

AutoClean is built around simple, intuitive concepts:

Workspace: Your personal folder (in Documents/Autoclean-EEG) containing all your custom tasks, configuration, and processing results.
Tasks: Pre-configured processing workflows for specific experiments (e.g., resting-state, auditory experiments). Each task contains all the settings and steps needed to process your data.
Pipeline: The processing engine that takes your data and task, then automatically handles all the complex EEG preprocessing steps.
Auto-Discovery: Simply drop task files into your workspace - AutoClean automatically finds and makes them available for use.

Quick Start Examples#

🎯 For Non-Technical Users (Command Line)

# Install AutoClean
pip install autocleaneeg

# Run first-time setup
autoclean setup

# Process your data (that's it!)
autoclean process RestingEyesOpen my_eeg_data.raw

🔧 For Technical Users (Python)

from autoclean import Pipeline

# Simple usage - uses your workspace automatically
pipeline = Pipeline()
pipeline.process_file("my_data.raw", "RestingEyesOpen")

# Custom output location
pipeline = Pipeline(output_dir="my_results/")
pipeline.process_file("my_data.raw", "CustomTask")