> ## Documentation Index
> Fetch the complete documentation index at: https://docs.autocleaneeg.org/llms.txt
> Use this file to discover all available pages before exploring further.

# Welcome to the AutocleanEEG Pipeline!

> Automated EEG Processing Software

<Note>
  **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](https://mne.tools/stable/index.html) 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](https://pylossless.readthedocs.io/en/latest/).

  The [principal investigator](https://scholar.google.com/citations?user=5vxtu0QAAAAJ\&hl=en) 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.
</Note>

<Info>
  **Prerequisites**:

  * [uv Python Package Manger](https://github.com/astral-sh/uv)
</Info>

## QuickStart

<Steps>
  <Step title="Install AutocleanEEG Pipeline">
    <CodeGroup>
      ```bash stable theme={null}
      uv tool install autocleaneeg-pipeline
      ```

      ```shell development theme={null}
      uv tool install git+https://github.com/cincibrainlab/autoclean_pipeline.git
      ```
    </CodeGroup>
  </Step>

  <Step title="Run AutocleanEEG Pipeline">
    ```bash theme={null}
    autocleaneeg-pipeline
    ```

    <img src="https://mintcdn.com/cincibrainlab/2x6X7lB8QORADI9R/images/welcome-autoclean-run.png?fit=max&auto=format&n=2x6X7lB8QORADI9R&q=85&s=df22206b0ae0110dce34b03da7cbd638" alt="AutocleanEEG CLI running" style={{ borderRadius: '0.5rem', marginTop: '0.75rem' }} width="1688" height="1196" data-path="images/welcome-autoclean-run.png" />

    <Note>
      AutocleanEEG’s welcome page highlights system details, workspace setup, key commands, and provides links to documentation and the code repository.
    </Note>
  </Step>

  <Step title="View AutocleanEEG Pipeline help">
    ```bash theme={null}
    autocleaneeg-pipeline help
    ```

    <img src="https://mintcdn.com/cincibrainlab/XNLEiR7_FsHlP2I2/images/welcome-help.png?fit=max&auto=format&n=XNLEiR7_FsHlP2I2&q=85&s=9570f8fb25e6da710c4ad8aff1b60b6a" alt="AutocleanEEG CLI help showing available commands" style={{ borderRadius: '0.5rem', marginTop: '0.75rem' }} width="1528" height="1160" data-path="images/welcome-help.png" />

    <Note>
      AutocleanEEG's help command displays all available commands including workspace configuration, file viewing, task management, data processing, review GUI, and authentication features.
    </Note>
  </Step>

  <Step title="View a file">
    ```bash theme={null}
    autocleaneeg-pipeline view /path/to/your_file.set
    ```

    <img src="https://mintcdn.com/cincibrainlab/VGcS015eUXaQcfyx/images/welcome-view.png?fit=max&auto=format&n=VGcS015eUXaQcfyx&q=85&s=2c0b18abe495cc7a928509815f4763ae" alt="AutocleanEEG viewer showing an EEG file" style={{ borderRadius: '0.5rem', marginTop: '0.75rem' }} width="2228" height="1592" data-path="images/welcome-view.png" />

    <Note>
      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](https://github.com/mne-tools/mne-qt-browser).
    </Note>
  </Step>
</Steps>