Agent skill · research science · k-dense-ai
neuropixels-analysis
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.
Why this skill is useful
Includes executable scripts for end-to-end analysis of Neuropixels data that aren't available in public documentation.
What it needs
Requires spikeinterface installed locally. About 7k tokens when loaded. Last updated 2026-08-03. 32,849 stars on the source repository.
What this skill does
Neuropixels Data Analysis Overview Toolkit for analyzing Neuropixels high-density neural recordings using current best practices from SpikeInterface, 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. 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 phaseshift 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.readspikeglx() Open Ephys .continuous, .oebin si.readopenephys() NWB .nwb si.readnwb() Quick Start Import and configure parallel processing Loading data Full pipeline (bundled script) The repository ships an end-to-end pipeline built on SpikeInterface: It performs load → preprocess → drift check → optional motion correction → sorting → postprocessing → quality metrics → curation → export. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills k-dense-ai/neuropixels-analysis