What is neuropixels-analysis?

A workflow for analyzing Neuropixels recordings, which are high-density probes that measure electrical activity from many neurons. It uses SpikeInterface to load, clean, sort, measure, and curate recorded neural signals.

Use it to process SpikeGLX, Open Ephys, or NWB data, correct drift, detect spikes, run spike-sorting methods, calculate unit-quality measures, and curate detected neurons.

Raw recordings need preprocessing, motion correction, spike sorting, and quality checks before individual neuron activity can be trusted. The workflow brings those stages together for several common recording formats and sorting tools.

neuropixels-analysis — Skill for Claude Code and Codex by agentlas-ai

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add agentlas-ai/agentlas-desktop --skill neuropixels-analysis

Clone the repo

git clone --depth 1 https://github.com/agentlas-ai/agentlas-desktop

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/neuropixels-analysis/github.svg)](https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/neuropixels-analysis)

Your own site

<a href="https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/neuropixels-analysis"><img src="https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/neuropixels-analysis/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/neuropixels-analysis"><img src="https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/neuropixels-analysis.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 98 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 4,307 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin 100% copy Near-identical to another mod in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00098	$0.04307
Opus 5.5	$0.00039	$0.01723
Sonnet 5.5	$0.00020	$0.00861
Haiku 4.5	$0.00010	$0.00431

Measured 1mo ago against content hash 3eadefe63c27, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

neuropixels-analysis scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.

The scan reads SKILL.md. This mod also ships 7 executable files (assets/analysis_template.py, scripts/compute_metrics.py, scripts/explore_recording.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

Origin

This is a copy

100% identical to neuropixels-analysis — 121 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

plugins/agentlas-science-skills/skills/neuropixels-analysis/SKILL.md · 430 lines

How it starts

The opening of the file, as written. The whole thing — 430 lines — stays where its author put it; the contents beside it link to each section on GitHub.

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 `phase_shift` 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.read_spikeglx()`
Open Ephys	`.continuous`, `.oebin`	`si.read_openephys()`
NWB	`.nwb`	`si.read_nwb()`

Quick Start

Import and configure parallel processing

import spikeinterface.full as si

# Global job kwargs are reused by all parallelizable steps
si.set_global_job_kwargs(n_jobs=-1, chunk_duration="1s", progress_bar=True)

Read the full file on GitHub · 430 lines

Files

What ships with it

17 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

1mo ago First seen · 430 lines · 98 tokens per session scan A 3eadefe63c27

Subscribe to this mod's changes

neuropixels-analysis is a skill published in the GitHub repository agentlas-ai/agentlas-desktop (6 stars, last pushed yesterday), licensed Apache-2.0. It adds 98 tokens to every session and 4,307 once invoked, about $0.0004 per session on Opus 5.5. A static security scan graded it A with 0 findings. It is 100% identical to neuropixels-analysis, differing in 121 lines, and is treated as a copy.

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