Neuropixels Analysis

An end-to-end SpikeInterface workflow for Neuropixels recordings: loading, preprocessing, drift correction, spike sorting, quality metrics, and unit curation.

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

Loads data from SpikeGLX (.ap.bin/.meta), Open Ephys, and NWB, with stream inspection first.
Preprocesses with the IBL-style chain: highpass filter → bad-channel detection/removal → phase_shift ADC correction (NP 1.0) → global median common reference → save to binary.
Checks and corrects drift via peak detection/localization, drift raster maps, and correct_motion presets (nonrigid_fast_and_accurate, dredge, etc.).
Runs spike sorting with Kilosort4 (CUDA GPU) or CPU sorters (SpykingCircus2, Tridesclous2, Mountainsort5), including containerized external sorters.
Computes quality metrics and curates: SNR, ISI violations, presence ratio, amplitude cutoff; Allen/IBL threshold presets, pretrained UnitRefine classifiers, and agent-assisted visual review of borderline units.
Exports to Phy, figure reports, NWB, and CSV metric tables.

Who it's for

Systems neuroscientists recording with Neuropixels 1.0/2.0 probes
Labs standardizing a reproducible SpikeInterface pipeline
Students and postdocs trying to cut down manual Phy curation time

Example uses

"Slice the first 60 s of this SpikeGLX run, plot the drift raster, and tell me whether motion correction is needed."
"Run scripts/neuropixels_pipeline.py with Kilosort4 and the allen curation preset, then hand me quality_metrics.csv."
"Apply the UnitRefine noise/neural classifier, then render waveforms and correlograms only for units with probability between 0.5 and 0.7 so I can judge them."

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/neuropixels-analysis/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)

Download the ZIP with the button below.
In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.

↓ Download ZIP

Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/neuropixels-analysis folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/neuropixels-analysis/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/neuropixels-analysis ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

Make sure you have Python 3.10+ and git installed (python --version).
Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
Copy the skill into place: mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/neuropixels-analysis ~/.claude/skills/
Install the core stack: uv pip install "spikeinterface[full]" probeinterface neo
Add a sorter: uv pip install kilosort if you have a CUDA GPU, otherwise uv pip install mountainsort5 for CPU sorting.
Optional extras: uv pip install huggingface_hub skops for model-based curation, and uv pip install anthropic plus export ANTHROPIC_API_KEY=... in your shell (never hardcode keys) for AI-assisted visual curation.
Restart Claude Code and ask something like "analyze this Neuropixels recording" to trigger the skill.

View source on GitHub ↗License: MIT