AIND Ephys Pipeline Documentation
=================================

Welcome to the AIND Ephys Pipeline documentation. This pipeline provides a comprehensive solution for electrophysiology data analysis using SpikeInterface.

.. toctree::
   :maxdepth: 3
   :caption: Contents:

   introduction
   architecture
   installation
   pipeline_steps
   input_output
   parameters
   deployments
   customization
   troubleshooting
   releases

Overview
--------

The AIND Ephys Pipeline is built on ``Nextflow`` and integrates multiple tools for electrophysiology data processing, 
from preprocessing through spike sorting to visualization and NWB export.

Quick Links
-----------

- `GitHub Repository <https://github.com/AllenNeuralDynamics/aind-ephys-pipeline>`_
- `SpikeInterface Documentation <https://spikeinterface.readthedocs.io/>`_
- `Nextflow Documentation <https://www.nextflow.io/docs/latest/index.html>`_