alterlab-neuropixels
CommunityEnd-to-end Neuropixels data analysis workflow
Education & Research#curation#preprocessing#quality-metrics#ai-assisted#neuropixels#spikeinterface#spike-sorting
AuthorAlterLab-IEU
Version1.0.0
Installs0
System Documentation
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.
Dependency Matrix
Required Modules
spikeinterfacepandasnumpymatplotlibprobeinterface
Components
scriptsreferencesassets
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: alterlab-neuropixels Download link: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/archive/main.zip#alterlab-neuropixels Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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