neuropixels_pipeline

Based on SpikeInterface, Allen Institute, and IBL recommendations.

Skills
Scientific
1

What it does and how to use it

A skill that teaches Claude Code to do scientific tasks well. It is packaged knowledge the model uses whenever it is relevant.

Install the skill (command above).
In Claude Code, describe what you need - the skill turns on by itself when the context fits.
No commands to memorize: you talk in plain language and the skill does the rest.

Install (Claude Code)

mkdir -p .claude/skills/neuropixels-pipeline && curl -fsSL https://doutorai.pt/data/lib/skills__neuropixels-pipeline.md -o .claude/skills/neuropixels-pipeline/SKILL.md

Paste this command into the terminal, in your project folder, and the component installs automatically.

Content

#!/usr/bin/env python3
"""
Neuropixels Data Analysis Pipeline (Best Practices Version)

Based on SpikeInterface, Allen Institute, and IBL recommendations.

Usage:
    python neuropixels_pipeline.py /path/to/spikeglx/data /path/to/output

References:
    - https://spikeinterface.readthedocs.io/en/stable/how_to/analyze_neuropixels.html
    - https://github.com/AllenInstitute/ecephys_spike_sorting
"""

import argparse
from pathlib import Path
import json
import spikeinterface.full as si
import numpy as np


def load_recording(data_path: str, stream_id: str = 'imec0.ap') -> si.BaseRecording:
    "

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