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Neuropixels Electrophysiology Analysis

Guides an agent through loading, cleaning, sorting and curating Neuropixels neural recordings

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
15 files

What it does

Teaches the agent a full workflow for Neuropixels brain-probe recordings: loading SpikeGLX, Open Ephys or NWB data, filtering and drift correction, spike sorting with tools such as Kilosort4, computing quality metrics, and curating units. The agent gets working SpikeInterface code plus bundled Python scripts to run quality metrics and quick exploration. It is aimed at researchers who already have raw electrophysiology data and want a consistent, documented pipeline.

Great for

  • Neuroscience labs processing Neuropixels 1.0 or 2.0 recordings
  • Students learning spike sorting and unit curation with SpikeInterface
  • Analysts who need a reviewed checklist for preprocessing and drift checks

Skip it if

  • Non-electrophysiology data or people without raw probe recordings, since the workflow assumes Neuropixels files and metadata
  • Producing publishable or clinical results without expert validation: the bundled curation thresholds are described as local screening presets, not reproductions of institutional pipelines, and sorter calls are marked illustrative until tested on your own data
  • Running on recordings you have not backed up, because the workflow writes preprocessed copies, motion outputs and sorting folders to disk

Try asking

  • “Load my SpikeGLX run folder, check drift, and show me a drift raster before sorting”
  • “Preprocess this Neuropixels 1.0 recording with high-pass filtering, bad-channel detection and phase shift”
  • “Compute quality metrics for my Kilosort4 output and screen units with the allen preset”
  • “Write a copy-and-edit analysis script for my Open Ephys session”
Step-by-step guide: how to use Neuropixels Electrophysiology AnalysisInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 15 original files, the MIT licence and an attribution note.

    neuropixels-analysis.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip neuropixels-analysis.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip neuropixels-analysis.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Validate the AP stream, calibration and channel geometry on a short slice (the 60 s example) before running full sorting
  • Choose one drift-correction stage only: either external motion correction or the sorter's internal correction, to avoid double correction
  • Treat the curation labels as screening output and review units manually in Phy or the report before using them

What's inside

  • assets/analysis_template.py
  • references/AI_CURATION.md
  • references/ANALYSIS.md
  • references/api_reference.md
  • references/AUTOMATED_CURATION.md
  • references/MOTION_CORRECTION.md
  • references/plotting_guide.md
  • references/PREPROCESSING.md
  • references/QUALITY_METRICS.md
  • references/SPIKE_SORTING.md
  • references/standard_workflow.md
  • scripts/_common.py
  • scripts/compute_metrics.py
  • scripts/explore_recording.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.