Neuropixels Analysis
Neuropixels neural recording analysis.
Install
npx skills add synthetic-sciences/openscience --skill neuropixels-analysis -g -a claude-code -y- Repository
- synthetic-sciences/openscience4.3k
- Category
- Engineering
- Updated
- 5d ago
- License
- MIT license
- Context cost
- Mediumabout 2,728 tokens
- Runs scripts
- Yes, review before use
What it does
Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.
Neuropixels Data Analysis
Overview
Comprehensive toolkit for analyzing Neuropixels high-density neural recordings using current best practices from SpikeInterface, Allen Institute, and International Brain Laboratory (IBL). Supports the full workflow from raw data to publication-ready curated units.
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, CAR, bad channel detection)
- Detecting and correcting motion/drift in recordings
- Running spike sorting (Kilosort4, SpykingCircus2, Mountainsort5)
- Computing quality metrics (SNR, ISI violations, presence ratio)
- Curating units using Allen/IBL criteria
- Creating visualizations of neural data
- Exporting results to Phy or NWB
Supported Hardware & Formats
| Probe | Electrodes | Channels | Notes |
|---|---|---|---|
| Neuropixels 1.0 | 960 | 384 | Requires phase_shift 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
Basic Import and Setup
import spikeinterface.full as si
import neuropixels_analysis as npa
# Configure parallel processing
job_kwargs = dict(n_jobs=-1, chunk_duration='1s', progress_bar=True)
Loading Data
# SpikeGLX (most common)
recording = si.read_spikeglx('/path/to/data', stream_id='imec0.ap')
# Open Ephys (common for many labs)
recording = si.read_openephys('/path/to/Record_Node_101/')
