autocleaneeg-pipeline 2.2.4

A modular framework for automated EEG data processing, built on MNE-Python

AutoCleanEEG Pipeline

A modular framework for automated EEG data processing, built on MNE-Python.

Features

• Framework for automated EEG preprocessing with "lego block" modularity
• Support for multiple EEG paradigms (ASSR, Chirp, MMN, Resting State)
• BIDS-compatible data organization and comprehensive quality control
• Extensible plugin system for file formats, montages, and event processing
• Research-focused workflow: single file testing → parameter tuning → batch processing
• Detailed output: logs (stored in your AutoClean workspace), stage files, metadata, and quality control visualizations

Installation (uv)

Use Astral's uv for fast, isolated installs. If you don't have uv yet, see https://docs.astral.sh/uv/

• Install CLI (recommended for users):

uv tool install autocleaneeg-pipeline
autocleaneeg-pipeline --help

• Upgrade or remove:

uv tool upgrade autocleaneeg-pipeline
uv tool uninstall autocleaneeg-pipeline

• Development install from source:

git clone https://github.com/cincibrainlab/autoclean_pipeline.git
cd autoclean_pipeline
uv venv && source .venv/bin/activate   # Windows: .venv\\Scripts\\activate
uv pip install -e .
# Optional extras
# uv pip install -e '.[gui]'   # GUI review tool dependencies
# uv pip install -e '.[docs]'  # Documentation tooling

Quick Start

Process a file using a built-in task:

autocleaneeg-pipeline process RestingEyesOpen /path/to/data.raw

List tasks and show overrides:

autocleaneeg-pipeline list-tasks --overrides

Task Commands

Common task management commands:

# List available tasks (built-in and workspace)
autocleaneeg-pipeline task list

# Generate a new task template in your workspace
autocleaneeg-pipeline task template

# Open tasks folder
autocleaneeg-pipeline task explore

# Edit a task by name or path
autocleaneeg-pipeline task edit <name|path>

# Import or copy tasks into the workspace
autocleaneeg-pipeline task import <path>
autocleaneeg-pipeline task copy <name|path>

# Manage active task
autocleaneeg-pipeline task set <name>
autocleaneeg-pipeline task show
autocleaneeg-pipeline task unset

Prefer a web wizard? TaskWizard: https://taskwizard.autocleaneeg.org/

Theme and Color

AutoClean’s CLI uses Rich with semantic styles and adaptive themes for readable output across light/dark terminals, limited color depth, and colorless logs.

• Flag: --theme auto|dark|light|hc|mono (default: auto)
  • mono: Monochrome (no hues), ideal for logs or unknown backgrounds
  • hc: High-contrast, accessible on both dark and light backgrounds
• Env overrides:
  • AUTOCLEAN_THEME=auto|dark|light|hc|mono
  • AUTOCLEAN_COLOR_DEPTH=auto|8|256|truecolor
  • NO_COLOR=1 disables color
  • FORCE_COLOR=1 forces color even in non-TTY (e.g., CI)

Examples:

autocleaneeg-pipeline --theme light list-tasks
AUTOCLEAN_THEME=hc autocleaneeg-pipeline version
NO_COLOR=1 autocleaneeg-pipeline list-tasks

Documentation

Full documentation is available at https://cincibrainlab.github.io/autoclean_pipeline/

Contributing

We welcome contributions! Please see our Contributing Guide for details.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Acknowledgments

• Cincinnati Children's Hospital Research Foundation
• Built with MNE-Python