neuropixels-analysis

Neuropixels Data Analysis

Overview

Toolkit for analyzing Neuropixels high-density neural recordings using current best practices from SpikeInterface, the Allen Institute, and the International Brain Laboratory (IBL). It covers the full workflow from raw data to publication-ready curated units.

All examples use the real SpikeInterface API (spikeinterface.full as si) plus the companion curation module (spikeinterface.curation as sc). The skill ships runnable scripts in scripts/ and a copy-and-edit template in assets/ that implement this workflow directly on top of SpikeInterface — there is no separate package to install beyond the dependencies listed under Installation.

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, common reference, bad-channel detection)
• Detecting and correcting motion/drift
• Running spike sorting (Kilosort4, SpykingCircus2, Mountainsort5, Tridesclous2)
• Computing quality metrics (SNR, ISI violations, presence ratio, amplitude cutoff)
• Curating units (threshold-based, model-based, or AI-assisted)
• Creating visualizations and exporting to Phy or NWB

Supported Hardware & Formats

Probe	Electrodes	Channels	Notes
Neuropixels 1.0	960	384	Use phase_shift for ADC 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

Import and configure parallel processing

import spikeinterface.full as si

# Global job kwargs are reused by all parallelizable steps
si.set_global_job_kwargs(n_jobs=-1, chunk_duration="1s", progress_bar=True)

Loading data

# Inspect available streams first
stream_names, stream_ids = si.get_neo_streams("spikeglx", "/path/to/run_g0/")
print(stream_names)  # e.g. ['imec0.ap', 'imec0.lf', 'nidq']

# SpikeGLX (most common) — select the AP stream by name
recording = si.read_spikeglx("/path/to/run_g0/", stream_name="imec0.ap", load_sync_channel=False)

# Open Ephys
recording = si.read_openephys("/path/to/Record_Node_101/")

# For quick iteration, slice the first 60 s
fs = recording.get_sampling_frequency()
recording_sub = recording.frame_slice(0, int(60 * fs))

Full pipeline (bundled script)

The repository ships an end-to-end pipeline built on SpikeInterface:

python scripts/neuropixels_pipeline.py /path/to/spikeglx/data output/ --sorter kilosort4 --curation allen

It performs load → preprocess → drift check → optional motion correction → sorting → postprocessing → quality metrics → curation → export. Read the steps below to run them interactively or customize the pipeline.

Standard Analysis Workflow

1. Preprocessing

Recommended chain, following the SpikeInterface Neuropixels how-to (IBL-style destriping with channel removal + common reference):

rec = si.highpass_filter(recording, freq_min=400.0)
bad_channel_ids, channel_labels = si.detect_bad_channels(rec)
rec = rec.remove_channels(bad_channel_ids)
rec = si.phase_shift(rec)  # ADC phase correction (Neuropixels 1.0)
rec = si.common_reference(rec, operator="median", reference="global")

Save the preprocessed recording (Kilosort needs a binary file, and it speeds up reuse):

rec = rec.save(folder="preprocessed/", format="binary")

2. Check and correct drift

Always inspect drift before sorting:

from spikeinterface.sortingcomponents.peak_detection import detect_peaks
from spikeinterface.sortingcomponents.peak_localization import localize_peaks

noise_levels = si.get_noise_levels(rec, return_in_uV=False)
peaks = detect_peaks(rec, method="locally_exclusive", noise_levels=noise_levels,
                     detect_threshold=5, radius_um=50.0)
peak_locations = localize_peaks(rec, peaks, method="center_of_mass")

# Visualize the drift raster
si.plot_drift_raster_map(peaks=peaks, peak_locations=peak_locations,
                         recording=rec, clim=(-50, 50))

Apply correction if needed (presets: rigid_fast, kilosort_like, nonrigid_accurate, nonrigid_fast_and_accurate, dredge, dredge_fast):

rec_corrected = si.correct_motion(rec, preset="nonrigid_fast_and_accurate", folder="motion/")

3. Spike sorting

# Kilosort4 (recommended, requires a CUDA GPU)
sorting = si.run_sorter("kilosort4", rec_corrected, folder="ks4_output")

# CPU alternatives (internally developed, no external install)
sorting = si.run_sorter("spykingcircus2", rec_corrected, folder="sc2_output")
sorting = si.run_sorter("tridesclous2", rec_corrected, folder="tdc2_output")
sorting = si.run_sorter("mountainsort5", rec_corrected, folder="ms5_output")

# External sorters can run in containers without local install
sorting = si.run_sorter("kilosort2_5", rec_corrected, folder="ks25_output", docker_image=True)

print(si.installed_sorters())

Note: run_sorter uses the folder= argument. The older output_folder= is deprecated.

4. Postprocessing

analyzer = si.create_sorting_analyzer(sorting, rec_corrected, sparse=True,
                                      format="binary_folder", folder="analyzer/")

analyzer.compute("random_spikes", method="uniform", max_spikes_per_unit=500)
analyzer.compute("waveforms", ms_before=1.0, ms_after=2.0)
analyzer.compute("templates", operators=["average", "std"])
analyzer.compute("noise_levels")
analyzer.compute("spike_amplitudes")
analyzer.compute("correlograms", window_ms=50.0, bin_ms=1.0)
analyzer.compute("unit_locations", method="monopolar_triangulation")
analyzer.compute("template_similarity")

metric_names = ["firing_rate", "presence_ratio", "snr", "isi_violation", "amplitude_cutoff"]
analyzer.compute("quality_metrics", metric_names=metric_names)
metrics = analyzer.get_extension("quality_metrics").get_data()

5. Curation by metric thresholds

# Allen-style query (note: column is isi_violations_ratio)
query = "(amplitude_cutoff < 0.1) & (isi_violations_ratio < 0.5) & (presence_ratio > 0.9)"
good_unit_ids = metrics.query(query).index.values

For reusable, multi-threshold logic with allen / ibl / strict presets, use the bundled scripts/compute_metrics.py. See references/AUTOMATED_CURATION.md for details and the Bombcell / UnitMatch tools.

6. Model-based curation (UnitRefine)

SpikeInterface can apply pretrained machine-learning classifiers from Hugging Face via the spikeinterface.curation module. The UnitRefine models were trained on real Neuropixels data (V1, SC, ALM):

import spikeinterface.curation as sc

# 1) noise vs neural
noise_labels = sc.model_based_label_units(
    sorting_analyzer=analyzer,
    repo_id="SpikeInterface/UnitRefine_noise_neural_classifier",
    trust_model=True,
)
neural = analyzer.remove_units(noise_labels[noise_labels["prediction"] == "noise"].index)

# 2) single-unit (sua) vs multi-unit (mua) on the surviving units
sua_mua_labels = sc.model_based_label_units(
    sorting_analyzer=neural,
    repo_id="SpikeInterface/UnitRefine_sua_mua_classifier",
    trust_model=True,
)

Each call returns a DataFrame with prediction and probability (confidence) per unit. trust_model=True (or an explicit trusted=[...] list) is required to load the .skops model — only load models from sources you trust. Models trained on other brain areas/datasets may not transfer; validate against a manually labelled subset.

7. AI-assisted curation (for uncertain units)

When running inside an agent such as Cursor or Claude Code, the agent can directly inspect waveform/correlogram plots and give an expert read — no API setup required. Generate plots and ask the agent to assess isolation quality.

For programmatic vision-model access, read API keys from the environment — never hardcode credentials in analysis scripts (they leak into version control and logs):

import os
from anthropic import Anthropic

client = Anthropic(api_key=os.environ["ANTHROPIC_API_KEY"])  # set this in your shell, not in code

See references/AI_CURATION.md for the full pattern (rendering a unit summary image, building the prompt, and parsing the response).

8. Export results

# Keep only good units, then export
analyzer_clean = analyzer.select_units(good_unit_ids, folder="analyzer_clean/", format="binary_folder")

# Phy for manual review
si.export_to_phy(analyzer_clean, output_folder="phy_export/",
                 compute_pc_features=True, compute_amplitudes=True)

# Figures report
si.export_report(analyzer_clean, "report/", format="png")

# NWB
from spikeinterface.exporters import export_to_nwb
export_to_nwb(analyzer_clean, "output.nwb")

# Metrics table
metrics.to_csv("quality_metrics.csv")

Common Pitfalls and Best Practices

1. Always check drift before spike sorting — drift > ~10 μm meaningfully degrades quality.
2. Use phase_shift for Neuropixels 1.0 to correct ADC sampling offsets.
3. Save the preprocessed recording with rec.save(folder=...) to avoid recomputation (Kilosort also needs a binary file).
4. Use a GPU for Kilosort4 — it is far faster than CPU sorters.
5. Review uncertain units — automated/model-based curation is a starting point, not a verdict.
6. Combine approaches — thresholds for clear cases, model/AI for borderline units.
7. Document thresholds and model repo IDs for reproducibility.
8. Export to Phy for critical experiments — human oversight is valuable.

Key Parameters to Adjust

Preprocessing

• freq_min: highpass cutoff (300–400 Hz typical)
• detect_bad_channels: returns (bad_channel_ids, channel_labels)

Motion Correction

• preset: nonrigid_fast_and_accurate (balanced), nonrigid_accurate (severe drift), dredge (state of the art)

Spike Sorting (Kilosort4)

• batch_size: samples per batch (60000 default)
• nblocks: drift blocks (increase for long, drifty recordings)
• Th_universal / Th_learned: detection thresholds (lower = more spikes)

Quality Metrics

• snr: signal-to-noise cutoff (3–5 typical)
• isi_violations_ratio: refractory violations (0.01–0.5)
• presence_ratio: recording coverage (0.5–0.95)

Bundled Resources

scripts/explore_recording.py

Quick inspection of a recording (streams, channels, duration, bad channels):

python scripts/explore_recording.py /path/to/data

scripts/preprocess_recording.py

Automated preprocessing:

python scripts/preprocess_recording.py /path/to/data --output preprocessed/

scripts/run_sorting.py

Run spike sorting:

python scripts/run_sorting.py preprocessed/ --sorter kilosort4 --output sorting/

scripts/compute_metrics.py

Compute quality metrics and apply curation:

python scripts/compute_metrics.py sorting/ preprocessed/ --output metrics/ --curation allen

scripts/export_to_phy.py

Export to Phy for manual curation:

python scripts/export_to_phy.py metrics/analyzer --output phy_export/

scripts/neuropixels_pipeline.py

Complete end-to-end pipeline (see Quick Start).

assets/analysis_template.py

Complete, editable analysis template. Copy and customize:

cp assets/analysis_template.py my_analysis.py
# Edit the PARAMETERS section, then run
python my_analysis.py

Detailed Reference Guides

Topic	Reference
Full workflow	references/standard_workflow.md
API reference (SpikeInterface)	references/api_reference.md
Plotting guide	references/plotting_guide.md
Preprocessing	references/PREPROCESSING.md
Spike sorting	references/SPIKE_SORTING.md
Motion correction	references/MOTION_CORRECTION.md
Quality metrics	references/QUALITY_METRICS.md
Automated & model-based curation	references/AUTOMATED_CURATION.md
AI-assisted curation	references/AI_CURATION.md
Waveform analysis	references/ANALYSIS.md

Installation

Requires Python ≥ 3.10. Using uv is recommended.

# Core packages (SpikeInterface bundles the curation/model tooling)
uv pip install "spikeinterface[full]" probeinterface neo

# Spike sorters
uv pip install kilosort          # Kilosort4 (CUDA GPU required)
uv pip install spykingcircus     # SpykingCircus (legacy; SpykingCircus2 ships with SpikeInterface)
uv pip install mountainsort5     # Mountainsort5 (CPU)

# Model-based curation (UnitRefine) downloads from Hugging Face
uv pip install "huggingface_hub" skops

# Optional: AI-assisted visual curation
uv pip install anthropic

# Optional: IBL tools and Bombcell
uv pip install ibl-neuropixel ibllib bombcell

For reproducible environments, pin versions (current as of 2026-06: spikeinterface==0.104.3, kilosort==4.1.7, probeinterface==0.3.2, neo==0.14.4). Unpinned installs are fine for quick experimentation but should be pinned in production pipelines.

Project Structure

project/
├── raw_data/
│   └── recording_g0/
│       └── recording_g0_imec0/
│           ├── recording_g0_t0.imec0.ap.bin
│           └── recording_g0_t0.imec0.ap.meta
├── preprocessed/           # Saved preprocessed recording
├── motion/                 # Motion estimation results
├── sorting_output/         # Spike sorter output
├── analyzer/               # SortingAnalyzer (waveforms, metrics)
├── phy_export/             # For manual curation
├── ai_curation/            # AI analysis reports
└── results/
    ├── quality_metrics.csv
    ├── curation_labels.json
    └── output.nwb

Additional Resources

• SpikeInterface Docs: https://spikeinterface.readthedocs.io/
• Neuropixels Tutorial: https://spikeinterface.readthedocs.io/en/stable/how_to/analyze_neuropixels.html
• Model-based Curation Tutorial: https://spikeinterface.readthedocs.io/en/stable/tutorials/curation/plot_1_automated_curation.html
• UnitRefine Models (Hugging Face): https://huggingface.co/SpikeInterface
• Kilosort4 GitHub: https://github.com/MouseLand/Kilosort
• IBL Neuropixel Tools: https://github.com/int-brain-lab/ibl-neuropixel
• Allen Institute ecephys: https://github.com/AllenInstitute/ecephys_spike_sorting
• Bombcell (Automated QC): https://github.com/Julie-Fabre/bombcell
• Awesome Neuropixels: https://github.com/Julie-Fabre/awesome_neuropixels

Agent operating procedure

1. Check the environment. Confirm tool versions, the reference genome/annotation build and the input formats (FASTQ, BAM, VCF, h5ad).
2. Pin down the inputs. Confirm formats, identifiers and parameters from the data or the user. Ask rather than guess any value that changes the result.
3. Run a small version first. Run the pipeline on a small subset (one sample, one chromosome, a few thousand cells) first.
4. Execute the full task using the instructions and references above.
5. Validate the result. Check QC metrics, sample identities, genome build consistency and batch effects before interpreting results.
6. Report. State what was run (versions, commands, parameters), what was checked, and what is still uncertain.

If this happens	Do this
Genome builds or identifiers do not match between inputs	Stop and harmonize (liftover, ID mapping) before continuing.
A function, flag or endpoint in these instructions is missing in the installed version	Check the installed version's own documentation (help(), --help, official docs), adapt, and tell the user. Never invent an API.
A required input, identifier or parameter is ambiguous	Ask the user, or state the assumption explicitly before running.

Integrity rules

• Never fabricate results, parameters, identifiers, citations or statistics. If something cannot be run or verified, say so plainly.
• Do not interpret biological significance beyond what the statistics support; report multiple-testing correction.
• Treat version-specific details here as possibly outdated: confirm them against the official documentation for the installed version.
• Ask before actions that cost money, consume shared GPUs or cloud quota, touch personal or patient data, or cannot be undone.

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