Skill · em Dados, IA e pesquisa

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…

Procedência

Origem: davila7/claude-code-templates
Caminho: cli-tool/components/skills/scientific/neuropixels-analysis
Versão fixada: 57f899e5394bb8ca166f38eacae8f0853cbfe033
Licença: MIT
Espelhado em 25/09/2026
nenhum download no Claude Code Templates (lido em 25/09/2026)

Antes de instalar

19 arquivos · 140,3 KB · inclui 7 scripts que executam: assets/analysis_template.py, scripts/compute_metrics.py, scripts/explore_recording.py, scripts/export_to_phy.py, scripts/neuropixels_pipeline.py, scripts/preprocess_recording.py, scripts/run_sorting.py

Instalar na sua CLI

O comando baixa a versão fixada (commit 57f899e) direto da origem, para a pasta que a CLI lê. Precisa de curl (macOS e Linux); no Windows não há comando, porque o Rook Labs é para macOS.

Claude Code

Neste projeto: instala em .claude/skills/neuropixels-analysis/.

d=".claude/skills/neuropixels-analysis"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/neuropixels-analysis"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/AI_CURATION.md" "$u/AI_CURATION.md" \
  -o "$d/ANALYSIS.md" "$u/ANALYSIS.md" \
  -o "$d/assets/analysis_template.py" "$u/assets/analysis_template.py" \
  -o "$d/AUTOMATED_CURATION.md" "$u/AUTOMATED_CURATION.md" \
  -o "$d/LICENSE.txt" "$u/LICENSE.txt" \
  -o "$d/MOTION_CORRECTION.md" "$u/MOTION_CORRECTION.md" \
  -o "$d/PREPROCESSING.md" "$u/PREPROCESSING.md" \
  -o "$d/QUALITY_METRICS.md" "$u/QUALITY_METRICS.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/plotting_guide.md" "$u/references/plotting_guide.md" \
  -o "$d/references/standard_workflow.md" "$u/references/standard_workflow.md" \
  -o "$d/scripts/compute_metrics.py" "$u/scripts/compute_metrics.py" \
  -o "$d/scripts/explore_recording.py" "$u/scripts/explore_recording.py" \
  -o "$d/scripts/export_to_phy.py" "$u/scripts/export_to_phy.py" \
  -o "$d/scripts/neuropixels_pipeline.py" "$u/scripts/neuropixels_pipeline.py" \
  -o "$d/scripts/preprocess_recording.py" "$u/scripts/preprocess_recording.py" \
  -o "$d/scripts/run_sorting.py" "$u/scripts/run_sorting.py" \
  -o "$d/SPIKE_SORTING.md" "$u/SPIKE_SORTING.md"

Global: instala em ~/.claude/skills/neuropixels-analysis/.

d="$HOME/.claude/skills/neuropixels-analysis"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/neuropixels-analysis"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/AI_CURATION.md" "$u/AI_CURATION.md" \
  -o "$d/ANALYSIS.md" "$u/ANALYSIS.md" \
  -o "$d/assets/analysis_template.py" "$u/assets/analysis_template.py" \
  -o "$d/AUTOMATED_CURATION.md" "$u/AUTOMATED_CURATION.md" \
  -o "$d/LICENSE.txt" "$u/LICENSE.txt" \
  -o "$d/MOTION_CORRECTION.md" "$u/MOTION_CORRECTION.md" \
  -o "$d/PREPROCESSING.md" "$u/PREPROCESSING.md" \
  -o "$d/QUALITY_METRICS.md" "$u/QUALITY_METRICS.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/plotting_guide.md" "$u/references/plotting_guide.md" \
  -o "$d/references/standard_workflow.md" "$u/references/standard_workflow.md" \
  -o "$d/scripts/compute_metrics.py" "$u/scripts/compute_metrics.py" \
  -o "$d/scripts/explore_recording.py" "$u/scripts/explore_recording.py" \
  -o "$d/scripts/export_to_phy.py" "$u/scripts/export_to_phy.py" \
  -o "$d/scripts/neuropixels_pipeline.py" "$u/scripts/neuropixels_pipeline.py" \
  -o "$d/scripts/preprocess_recording.py" "$u/scripts/preprocess_recording.py" \
  -o "$d/scripts/run_sorting.py" "$u/scripts/run_sorting.py" \
  -o "$d/SPIKE_SORTING.md" "$u/SPIKE_SORTING.md"

Codex

Neste projeto: instala em .agents/skills/neuropixels-analysis/.

d=".agents/skills/neuropixels-analysis"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/neuropixels-analysis"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/AI_CURATION.md" "$u/AI_CURATION.md" \
  -o "$d/ANALYSIS.md" "$u/ANALYSIS.md" \
  -o "$d/assets/analysis_template.py" "$u/assets/analysis_template.py" \
  -o "$d/AUTOMATED_CURATION.md" "$u/AUTOMATED_CURATION.md" \
  -o "$d/LICENSE.txt" "$u/LICENSE.txt" \
  -o "$d/MOTION_CORRECTION.md" "$u/MOTION_CORRECTION.md" \
  -o "$d/PREPROCESSING.md" "$u/PREPROCESSING.md" \
  -o "$d/QUALITY_METRICS.md" "$u/QUALITY_METRICS.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/plotting_guide.md" "$u/references/plotting_guide.md" \
  -o "$d/references/standard_workflow.md" "$u/references/standard_workflow.md" \
  -o "$d/scripts/compute_metrics.py" "$u/scripts/compute_metrics.py" \
  -o "$d/scripts/explore_recording.py" "$u/scripts/explore_recording.py" \
  -o "$d/scripts/export_to_phy.py" "$u/scripts/export_to_phy.py" \
  -o "$d/scripts/neuropixels_pipeline.py" "$u/scripts/neuropixels_pipeline.py" \
  -o "$d/scripts/preprocess_recording.py" "$u/scripts/preprocess_recording.py" \
  -o "$d/scripts/run_sorting.py" "$u/scripts/run_sorting.py" \
  -o "$d/SPIKE_SORTING.md" "$u/SPIKE_SORTING.md"

Global: instala em ~/.agents/skills/neuropixels-analysis/.

d="$HOME/.agents/skills/neuropixels-analysis"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/neuropixels-analysis"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/AI_CURATION.md" "$u/AI_CURATION.md" \
  -o "$d/ANALYSIS.md" "$u/ANALYSIS.md" \
  -o "$d/assets/analysis_template.py" "$u/assets/analysis_template.py" \
  -o "$d/AUTOMATED_CURATION.md" "$u/AUTOMATED_CURATION.md" \
  -o "$d/LICENSE.txt" "$u/LICENSE.txt" \
  -o "$d/MOTION_CORRECTION.md" "$u/MOTION_CORRECTION.md" \
  -o "$d/PREPROCESSING.md" "$u/PREPROCESSING.md" \
  -o "$d/QUALITY_METRICS.md" "$u/QUALITY_METRICS.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/plotting_guide.md" "$u/references/plotting_guide.md" \
  -o "$d/references/standard_workflow.md" "$u/references/standard_workflow.md" \
  -o "$d/scripts/compute_metrics.py" "$u/scripts/compute_metrics.py" \
  -o "$d/scripts/explore_recording.py" "$u/scripts/explore_recording.py" \
  -o "$d/scripts/export_to_phy.py" "$u/scripts/export_to_phy.py" \
  -o "$d/scripts/neuropixels_pipeline.py" "$u/scripts/neuropixels_pipeline.py" \
  -o "$d/scripts/preprocess_recording.py" "$u/scripts/preprocess_recording.py" \
  -o "$d/scripts/run_sorting.py" "$u/scripts/run_sorting.py" \
  -o "$d/SPIKE_SORTING.md" "$u/SPIKE_SORTING.md"

Antigravity

Neste projeto: instala em .agents/skills/neuropixels-analysis/.

d=".agents/skills/neuropixels-analysis"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/neuropixels-analysis"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/AI_CURATION.md" "$u/AI_CURATION.md" \
  -o "$d/ANALYSIS.md" "$u/ANALYSIS.md" \
  -o "$d/assets/analysis_template.py" "$u/assets/analysis_template.py" \
  -o "$d/AUTOMATED_CURATION.md" "$u/AUTOMATED_CURATION.md" \
  -o "$d/LICENSE.txt" "$u/LICENSE.txt" \
  -o "$d/MOTION_CORRECTION.md" "$u/MOTION_CORRECTION.md" \
  -o "$d/PREPROCESSING.md" "$u/PREPROCESSING.md" \
  -o "$d/QUALITY_METRICS.md" "$u/QUALITY_METRICS.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/plotting_guide.md" "$u/references/plotting_guide.md" \
  -o "$d/references/standard_workflow.md" "$u/references/standard_workflow.md" \
  -o "$d/scripts/compute_metrics.py" "$u/scripts/compute_metrics.py" \
  -o "$d/scripts/explore_recording.py" "$u/scripts/explore_recording.py" \
  -o "$d/scripts/export_to_phy.py" "$u/scripts/export_to_phy.py" \
  -o "$d/scripts/neuropixels_pipeline.py" "$u/scripts/neuropixels_pipeline.py" \
  -o "$d/scripts/preprocess_recording.py" "$u/scripts/preprocess_recording.py" \
  -o "$d/scripts/run_sorting.py" "$u/scripts/run_sorting.py" \
  -o "$d/SPIKE_SORTING.md" "$u/SPIKE_SORTING.md"

Global: instala em ~/.gemini/antigravity-cli/skills/neuropixels-analysis/.

d="$HOME/.gemini/antigravity-cli/skills/neuropixels-analysis"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/neuropixels-analysis"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/AI_CURATION.md" "$u/AI_CURATION.md" \
  -o "$d/ANALYSIS.md" "$u/ANALYSIS.md" \
  -o "$d/assets/analysis_template.py" "$u/assets/analysis_template.py" \
  -o "$d/AUTOMATED_CURATION.md" "$u/AUTOMATED_CURATION.md" \
  -o "$d/LICENSE.txt" "$u/LICENSE.txt" \
  -o "$d/MOTION_CORRECTION.md" "$u/MOTION_CORRECTION.md" \
  -o "$d/PREPROCESSING.md" "$u/PREPROCESSING.md" \
  -o "$d/QUALITY_METRICS.md" "$u/QUALITY_METRICS.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/plotting_guide.md" "$u/references/plotting_guide.md" \
  -o "$d/references/standard_workflow.md" "$u/references/standard_workflow.md" \
  -o "$d/scripts/compute_metrics.py" "$u/scripts/compute_metrics.py" \
  -o "$d/scripts/explore_recording.py" "$u/scripts/explore_recording.py" \
  -o "$d/scripts/export_to_phy.py" "$u/scripts/export_to_phy.py" \
  -o "$d/scripts/neuropixels_pipeline.py" "$u/scripts/neuropixels_pipeline.py" \
  -o "$d/scripts/preprocess_recording.py" "$u/scripts/preprocess_recording.py" \
  -o "$d/scripts/run_sorting.py" "$u/scripts/run_sorting.py" \
  -o "$d/SPIKE_SORTING.md" "$u/SPIKE_SORTING.md"

Peça ao Rook

Já usa o Rook Labs? Cole no chat do Rook: instale a skill https://rooklabs.sh/marketplace/cct.neuropixels-analysis

Prévia do SKILL.md

---
name: neuropixels-analysis
description: "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, ex…
---

# Neuropixels Data Analysis

## Overview

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.

## 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

| Probe | Electrodes | Channels | Notes |
|-------|-----------|----------|-------|
| Neuropixels 1.0 | 960 | 384 | Requires phase_shift 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
…

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