neuropixels-analysis

The saved excerpt is a snapshot from review. The external source remains the complete and most current version.

---
name: neuropixels-analysis
description: Analyze Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB data, preprocessing, drift/motion correction, Kilosort4 (and CPU) spike sorting, quality metrics, and unit curation (threshold-based, model-based UnitRefine, and AI-assisted visual review). Use when working with Neuropixels 1.0/2.0 recordings, spike sorting, or extracellular electrophysiology analysis.
license: MIT license
metadata:
  version: "2.3"
  skill-author: K-Dense Inc.
  openclaw:
    primaryEnv: ANTHROPIC_API_KEY
    envVars:
    - name: ANTHROPIC_API_KEY
      required: false
      description: For optional Claude API calls.
---

# Neuropixels Data Analysis

## Overview

Toolkit for analyzing Neuropixels high-density neural recordings using current best
practices from [SpikeInterface](https://spikeinterface.readthedocs.io/), the Allen
Institute, and the International Brain Laboratory (IBL). It covers the full workflow from
raw data to publication-ready curated units.

All examples use the real SpikeInterface API (`spikeinterface.full as si`) plus the
companion curation module (`spikeinterface.curation as sc`). The skill ships runnable
scripts in `scripts/` and a copy-and-edit template in `assets/` that implement this
workflow directly on top of SpikeInterface — there is no separate package to install
beyond the dependencies listed under [Installation](#installation).

## When to Use This Skill

This skill should be used when:
- Working with Neuropixels recordings (`.ap.bin`, `.lf.bin`, `.meta` files)
- Loading data from SpikeGLX, Open Ephys, or NWB formats
- Preprocessing neural recordings (filtering, common reference, bad-channel detection)
- Detecting and correcting motion/drift
- Running spike sorting (Kilosort4, SpykingCircus2, Mountainsort5, Tridesclous2)
- Computing quality metrics (SNR, ISI violations, presence ratio, amplitude cutoff)
- Curating units (threshold-based, model-based, or AI-assisted)
- Creating visualizations and exporting to Phy or NWB

## Supported Hardware & Formats

| Probe | Electrodes | Channels | Notes |
|-------|-----------|----------|-------|
| Neuropixels 1.0 | 960 | 384 | Use `phase_shift` for ADC correction |
| Neuropixels 2.0 (single) | 1280 | 384 | Denser geometry |
| Neuropixels 2.0 (4-shank) | 5120 | 384 | Multi-region recording |

| Format | Extension | Reader |
|--------|-----------|--------|
| SpikeGLX | `.ap.bin`, `.lf.bin`, `.meta` | `si.read_spikeglx()` |
| Open Ephys | `.continuous`, `.oebin` | `si.read_openephys()` |
| NWB | `.nwb` | `si.read_nwb()` |

## Quick Start

### Import and configure parallel processing

```python
import spikeinterface.full as si

# Global job kwargs are reused by all parallelizable steps
si.set_global_job_kwargs(n_jobs=-1, chunk_duration="1s", progress_bar=True)
```

### Loading data

```python
# Inspect available streams first
stream_names, stream_ids = si.get_neo_streams("spikeglx", "/path/to/run_g0/")
print(stream_names)  # e.g. ['imec0.ap', 'imec0.lf', 'nidq']

# SpikeGLX (most common) — select the AP stream by name
recording = si.read_spikeglx("/path/to/run_g0/", stream_name="imec0.ap", load_sync_channel=False)

# Open Ephys
recording = si.read_openephys("/path/to/Record_Node_101/")

# For quick iteration, slice the first 60 s
fs = recording.get_sampling_frequency()
recording_sub = recording.frame_slice(0, int(60 * fs))
```

### Full pipeline (bundled script)

The repository ships an end-to-end pipeline built on SpikeInterface:

```bash
python scripts/neuropixels_pipeline.py /path/to/spikeglx/data output/ --sorter kilosort4 --curation allen
```

It performs load → preprocess → drift check → optional motion correction → sorting →
postprocessing → quality metrics → curation → export. Read the steps below to run them
interactively or customize the pipeline.

## Standard Analysis Workflow

### 1. Preprocessing

Recommended chain, following the SpikeInterface Neuropixels how-to (IBL-styl