Neuropixels-Analysis (Claude Skill)

Claude skill for high-density extracellular electrophysiology pipelines on Neuropixels probes, following SpikeInterface, Allen Institute, and International Brain Laboratory best practices.

   
Type Claude Skill
Supplier K-Dense Inc. (community OSS)
Availability GA — distributed with the K-Dense marketplace at v2.27.0
Pricing Free / OSS
Capabilities Read/Write — local computation on user-supplied recordings; GPU recommended for Kilosort4

How to install

  • Also packaged in the SciAgent-Skills collection (jaechang-hits (community OSS, CC BY 4.0)): clone jaechang-hits/SciAgent-Skills and run /plugin install sciagent-skills in Claude Code (or copy skills/scientific-computing/neuropixels-analysis into ~/.claude/skills/).
  • Claude Code / Claude.ai — Skills CLI (recommended): 
    npx skills add K-Dense-AI/scientific-agent-skills

    Installs the K-Dense collection; enable the neuropixels-analysis skill when prompted (also works in Cursor/Codex via the Agent Skills spec; requires Node ≥ 18).

  • Claude Code / Claude Desktop — manual clone: 
    git clone https://github.com/K-Dense-AI/scientific-agent-skills
cp -r scientific-agent-skills/skills/neuropixels-analysis ~/.claude/skills/

What it does

  • Loads recordings from SpikeGLX, Open Ephys, and NWB
  • Preprocessing: highpass filtering, Neuropixels 1.0 phase-shift correction, bad-channel detection, common-average referencing
  • Motion / drift estimation and correction (kilosort_like and nonrigid_accurate presets)
  • Spike sorting integration: Kilosort4 (GPU), SpykingCircus2, Mountainsort5 (CPU)
  • AI-assisted curation toward publication-ready single units

Primary use cases: Raw-to-curated-units pipelines on Neuropixels recordings, drift-corrected sorting on long sessions, cross-sorter comparison via SpikeInterface.

Notes

Kilosort4 needs a CUDA-capable GPU; SpykingCircus2 and Mountainsort5 fall back to CPU. The skill assumes SpikeInterface installed in the environment.

Sources

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