neuropixels-analysis

Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.

1.37x

Quality

86%

Does it follow best practices?

Impact

91%

1.37x

Average score across 3 eval scenarios

Securityby

Passed

No known issues

Evaluation results

96%

18%

Neuropixels Recording Preprocessing Script

NP1.0 preprocessing chain

Criteria

Without context

With context

Standard imports

50%

SpikeGLX loader

70%

100%

Phase shift applied

100%

Highpass or bandpass filter

100%

Bad channel detection

100%

Bad channel removal

100%

Median common reference

100%

Parallel processing

100%

Save preprocessed data

100%

No phase shift for NP2

100%

44%

Spike Sorting Pipeline with Drift Handling

Drift assessment and correction

Criteria

Without context

With context

Drift estimated before sorting

57%

100%

Drift visualized

100%

10-micron threshold

100%

kilosort_like for estimation

100%

nonrigid_accurate for correction

100%

Conditional correction

100%

Kilosort4 preference

100%

CPU alternative noted

44%

100%

No whitening before peak detection

100%

78%

14%

Unit Curation Script for Publication-Quality Dataset

Quality metrics and AI curation

Criteria

Without context

With context

Allen presence_ratio threshold

100%

Allen isi_violations threshold

100%

Allen amplitude_cutoff threshold

100%

Uncertain unit SNR range

100%

AI model selection

Metrics-first classification

100%

Analyzer extensions computed

100%

Save quality metrics CSV

100%

Save curation labels JSON

100%

sparse=True analyzer

Repository: K-Dense-AI/claude-scientific-skills
Commit: b58ad7e

Evaluated: 27 days ago
Agent: Claude Code
Model: Claude Sonnet 4.6

Table of Contents

Neuropixels Recording Preprocessing Script Spike Sorting Pipeline with Drift Handling Unit Curation Script for Publication-Quality Dataset

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