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Neuropixels-Analysis

Maintainer K-Dense Inc. · Last updated April 1, 2026

Comprehensive toolkit for analy.

Claude CodeOpenClawNanoClawAnalysisReproductionneuropixels-analysisneurosciencepackageneuroscience & electrophysiology

Original source

K-Dense-AI/claude-scientific-skills

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/neuropixels-analysis

Maintainer
K-Dense Inc.
License
MIT license
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Comprehensive toolkit for analyzing Neuropixels high-density neural recordings using current best practices from SpikeInterface, Allen Institute, and International Brain Laboratory (IBL). Supports the full workflow from raw data to publication-ready curated units.
  • job_kwargs = dict(n_jobs=-1, chunk_duration='1s', progress_bar=True).

Source Doc

Excerpt From SKILL.md

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, CAR, bad channel detection)
  • Detecting and correcting motion/drift in recordings
  • Running spike sorting (Kilosort4, SpykingCircus2, Mountainsort5)
  • Computing quality metrics (SNR, ISI violations, presence ratio)
  • Curating units using Allen/IBL criteria
  • Creating visualizations of neural data
  • Exporting results to Phy or NWB

Supported Hardware & Formats

ProbeElectrodesChannelsNotes
Neuropixels 1.0960384Requires phase_shift correction
Neuropixels 2.0 (single)1280384Denser geometry
Neuropixels 2.0 (4-shank)5120384Multi-region recording
FormatExtensionReader
SpikeGLX.ap.bin, .lf.bin, .metasi.read_spikeglx()
Open Ephys.continuous, .oebinsi.read_openephys()
NWB.nwbsi.read_nwb()

Basic Import and Setup

import spikeinterface.full as si
import neuropixels_analysis as npa

Use cases

  • Working with Neuropixels recordings (.ap.bin,.lf.bin,.meta files).
  • Loading data from SpikeGLX, Open Ephys, or NWB formats.
  • Preprocessing neural recordings (filtering, CAR, bad channel detection).
  • Detecting and correcting motion/drift in recordings.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

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