skills.rest
AlterLab-IEU
AlterLab-IEUCOMMUNITY
Explore all skills by this author →
GitHub

alterlab-neuropixels

Process Neuropixels recordings from raw data to curated units.

58|9|Updated Mar 16, 2026
Search Tags:#curation#preprocessing#quality-metrics#ai-assisted#neuropixels#spikeinterface#spike-sorting
One-click install
npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-neuropixels
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: alterlab-neuropixels
Source: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-neuropixels
Command: npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-neuropixels

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires spikeinterface, pandas, numpy, matplotlib, probeinterface, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

Neuropixels Data Analysis for end-to-end processing of Neuropixels data, from raw recordings to curated neuronal units across NP1.0/NP2.0, enabling researchers to generate publication-ready results with AI-assisted curation.

Core Features & Use Cases

  • Load and preprocess data from SpikeGLX/Open Ephys/NWB formats.
  • Apply motion/drift correction, spike sorting (Kilosort4, SpykingCircus, Mountainsort5), and quality metrics per Allen/IBL criteria.
  • AI-assisted curation with Claude Vision for rapid, visual quality assessments.
  • Export results to Phy, NWB, and generate publication-quality figures and reports.
  • Use cases include electrophysiology studies, neural decoding pipelines, and cross-protocol data curation.

Quick Start

Run the Neuropixels pipeline on your dataset by calling the neuropixels_pipeline.py script with the path to your data and an output directory.

Frequently Asked Questions about alterlab-neuropixels

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I run spike sorting on Neuropixels data from SpikeGLX or Open Ephys?▼

To process Neuropixels data end-to-end, call the neuropixels_pipeline.py script with your raw data path and output directory to execute preprocessing, motion correction, spike sorting, and curation automatically.

What is AI-assisted curation for spike sorting results?▼

AI-assisted curation uses Claude Vision to perform rapid visual quality assessments of sorted units, accelerating the identification of high-quality neuronal units according to Allen and IBL criteria.

Can I apply SpikeInterface preprocessing to NWB format recordings?▼

Yes, SpikeInterface preprocessing can be applied to NWB format recordings, alongside SpikeGLX and Open Ephys data, loading them directly into the end-to-end Neuropixels analysis pipeline.

Does this workflow support motion correction and drift correction for NP2.0 probes?▼

Yes, the workflow supports motion and drift correction for both NP1.0 and NP2.0 probes, applying SpikeInterface components to handle varying data conditions and improve sorting accuracy.

How do I export curated spike sorting results to Phy and NWB?▼

You can export curated spike sorting results to Phy and NWB formats, and generate publication-quality figures and reports, directly through the pipeline's built-in export options.

Related Skills

Explore More Education & Research Skills→
K-Dense-AIK-Dense-AI
33.0k

neuropixels-analysis

Process Neuropixels recordings into spike-sorted units with quality metrics.

Official
Advanced
hxk622hxk622
8

neuropixels-analysis

Analyze Neuropixels recordings with SpikeInterface and Kilosort4.

Community
Advanced
xjtulycxjtulyc
33

spike-sorting

Automate spike sorting of extracellular multi-electrode recordings into single-unit spike trains.

Community
Advanced
yunseo-kimyunseo-kim
1

strategy-advisor

Analyze business situations and generate strategic options with implementation considerations.

Community
Intermediate