Agent skill · research science · aiskillstore
neuropixels-analysis
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.
Why this skill is useful
Adds a complete analysis pipeline for Neuropixels data, including preprocessing, spike sorting, and quality metrics that are not commonly found in public resources.
What it needs
Requires neuropixels_analysis, spikeinterface installed locally. About 5k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
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 phaseshift 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.readspikeglx() Open Ephys .continuous, .oebin si.readopenephys() NWB .nwb si.readnwb() Quick Start Basic Import and Setup Loading Data Complete Pipeline (One Command) Standard Analysis Workflow 1. Preprocessing 2. Check and Correct Drift 3. Spike Sorting 4. Postprocessing 5. Curation 6. AI-Assisted Curation (For Uncertain Units) When using this skill with Claude Code, Claude can directly analyze waveform plots and provide expert curation decisions. For programmatic API access: Claude Code Integration: When running within Claude Code, ask Claude to examine waveform/correlogram plots directly - no API setup required. 7. Generate Analysis Report 8. Export Results Common Pitfalls and Best Practices 1. Always check drift before spike sorting - drift > 10μm significantly impacts quality 2. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/neuropixels-analysis