AIND Ephys Pipeline Documentation

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

Contents:

• Introduction
  • Key Concepts
  • Key Features
• Pipeline Architecture
  • Detailed Architecture Diagram
  • Architecture Components
    • Deployment Modes
    • Infrastructure Components
    • Data Flow
    • Version Control
    • Pipeline Steps Detailed Breakdown
• Installation
  • Requirements
    • Local Deployment
    • SLURM Deployment
  • Installation Steps
    • Local Setup
    • SLURM Setup
  • Clone the Repository
• Pipeline Steps
  • Job Dispatch
  • Preprocessing
  • Spike Sorting
  • Postprocessing
  • Curation
  • Visualization
  • Result Collection
  • NWB Export
• Input and Output
  • Input Data Types
    • SpikeGLX
    • Open Ephys
    • NWB
    • SpikeInterface
    • AIND
  • Pipeline Output
    • preprocessed/
    • spikesorted/
    • curated/
    • postprocessed/
    • nwb/
    • visualization/
  • Additional Files
• Pipeline Parameters
  • Global Parameters
  • Parameter File
  • Parameter Editor Webapp
  • JSON Schema
  • Process-Specific Arguments
    • Job Dispatch Parameters
    • Preprocessing Parameters
    • Spike Sorting Parameters
    • Postprocessing Parameters
    • Curation Parameters
    • NWB Ecephys Parameters
    • Visualization Parameters
  • Full example with custom parameters
• Deployment Options
  • SLURM Deployment
    • Requirements
    • Configuration
  • Local Deployment
    • Requirements
    • Running Locally
  • Code Ocean Deployment (AIND)
    • Main Branches
    • Optogenetics Branches
• Customization
  • Customizing Pipeline Steps
    • Custom Data Ingestion (job_dispatch)
  • Custom pre-processing
    • Providing a custom preprocessing pipeline
    • Preprocess data externally
  • Custom Spike Sorting
  • Custom postprocessing
• Troubleshooting
  • ERROR ~ Script compilation failed
  • OSError: Unable to synchronously open file
  • NUMBA cache issue: RuntimeError: cannot cache function
  • OSError: Read-only file system error
• Releases
  • 1.2.2 - May 28th 2026
    • Package versions
  • 1.2.1 - May 21st 2026
    • Package versions
  • 1.2.0 - May 8th 2026
    • Package versions
  • 1.1.1 - April 24th 2026
    • Bug fixes
  • 1.1.0 - April 2026
    • Package versions
    • Bug fixes
  • 1.0.0 - August 2025
    • Package versions
    • Bug fixes
    • New features
  • si-0.102.1 - March 2025
    • Package versions
    • Bug fixes
    • New features
  • si-0.101.2 - November 2024
    • Package versions
    • Bug fixes
    • New features
  • si-0.100.7 - February 2024
    • Package versions

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

• SpikeInterface Documentation

• Nextflow Documentation