Ready to supercharge your AI agents?

Install any skill in seconds. Free to start, no credit card required.

Neuropixels Data Analysis · k-dense-ai | DecimalAI

scienceby k-dense-ai

Neuropixels Data Analysis

k-dense-ai/neuropixels-analysis

Source k-dense-ai/scientific-agent-skills ↗License MIT

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).

SkillScore95Maintained

Automatic

Research pack

Last verified 9/8/2026

What it changes

Passed 20 of 21 test cases with the skill, and 10 of 21 without it.

Without skill45%

With skill95%

Checks it passed that the model alone missed

The CLI invocation passes --curation allen.
The query tests the column isi_violations_ratio.
The command runs scripts/neuropixels_pipeline.py.

and 16 more in the full report

11 fixed10 passed either way1 still failing0 broke

Pass-rate lift: +50 pp
Tokens: +160%
Agent turns: 0%
Response time: -15%

Model gemini-3.6-flashMeasured 9/8/2026v2 · latest is v321 of 22 cases passed with skill · 21 comparable

Tokens, turns and time describe resource use, not a dollar price.

This benchmark measured an earlier version of the skill.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/k-dense-ai-neuropixels-analysis/SKILL.md https://app.decimal.ai/s/k-dense-ai-neuropixels-analysis/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add k-dense-ai-neuropixels-analysis, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/k-dense-ai-neuropixels-analysis/ and pins it in .decimal/skills.lock

decimalai skills add k-dense-ai-neuropixels-analysis

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/k-dense-ai-neuropixels-analysis/SKILL.md https://app.decimal.ai/s/k-dense-ai-neuropixels-analysis/SKILL.md

Raw file: /s/k-dense-ai-neuropixels-analysis/SKILL.md ↗ · machine-readable summary at /s/k-dense-ai-neuropixels-analysis.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 10 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 10

Prompt

Which function and sub-module within SpikeInterface should be used to export curated sorting results to NWB format?

What was checked, without and with the skill
Checked	Without skill	With skill
Function export_to_nwb is imported from spikeinterface.exporters.	Missed	Passed
The export function receives the clean sorting analyzer.	Missed	Passed

case-16 · gemini-3.6-flash · 9/8/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md447 lines19 filesincludes scripts

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 reviewed, curated units. Targets SpikeInterface 0.105.0, ProbeInterface 0.4.0 and Neo 0.14.5 (reviewed 2026-10-01). Synthetic tests cover recording contracts, preprocessing, analyzers, metrics and exports; real acquisition files, native sorters, GPU execution and pretrained models remain illustrative.

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 acquisition ADC timing metadata
Neuropixels 2.0 (single)	1280	384	Verify part number and timing metadata
Neuropixels 2.0 (4-shank)	5120	384	Multi-region recording

Format	Extension	Reader

Track record

Benchmark

20 / 21

test cases passed, vs 10 / 21 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v5 — 10/8/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

k-dense-ai / scientific-agent-skills

skills/neuropixels-analysis/SKILL.md

View on GitHub ↗

License MIT licenseImported 10/8/2026Version v3Bundled 18 files · scripts

Other skills for the same job

Published skills whose descriptions closely match this one, with their headline benchmark lift.

More skills from the same source and nearby in the registry, with their headline benchmark lift.

Ready to supercharge your AI agents?

See it in action

What's inside

Neuropixels Data Analysis

Overview

When to Use This Skill

Supported Hardware & Formats

Track record

Benchmark

Adoption

SkillSafety

Source

Other skills for the same job

Related skills