neuropixels-analysis

Neuropixels Analysis

Overview

Neuropixels probes record extracellular voltage from 384 (NP 1.0) or 192 (NP 2.0) simultaneously recorded channels at 30 kHz. Analysis follows a canonical pipeline: raw data → spike sorting (Kilosort) → quality curation → unit analysis. SpikeInterface (Python) provides a unified API across 10+ spike sorters, handles data loading from multiple formats (SpikeGLX, OpenEphys, NWB), computes quality metrics, and exports sorted results. ProbeInterface manages probe geometry and channel maps. Post-sort analysis (PSTHs, firing rate, decoding) uses standard Python scientific stack.

When to Use

• Spike-sorting Neuropixels recordings from SpikeGLX (.bin) or OpenEphys (.dat) to extract single-unit activity
• Applying automatic quality control metrics (ISI violations, SNR, firing rate) to curate sorted units
• Computing peristimulus time histograms (PSTHs) locked to experimental events
• Analyzing population coding: decoding stimulus or behavioral variables from firing rates
• Converting sorted data to NWB (Neurodata Without Borders) format for sharing
• Comparing multiple spike sorters on the same dataset for method validation
• Visualizing unit waveforms, auto-correlograms, and spatial distribution across probe channels
• Use SpikeInterface instead for a unified framework that supports 10+ spike sorters with a common API and comparison tools

Prerequisites

• Python packages: spikeinterface[full], probeinterface, numpy, pandas, matplotlib, scipy
• Spike sorter: Kilosort4 (Python, pip install kilosort); or MATLAB-based Kilosort2/3 (requires MATLAB license)
• Data requirements: raw .bin (SpikeGLX) or .dat (OpenEphys) recording; probe channel map file (.prb or from ProbeInterface)
• Hardware: NVIDIA GPU (4+ GB VRAM) required for Kilosort; CPU fallback available but ~10× slower

pip install spikeinterface[full] probeinterface kilosort
# Optional: Phy for manual curation
pip install phy

Workflow

Step 1: Load Raw Recording

import spikeinterface.full as si
from pathlib import Path

# SpikeGLX recording (most common Neuropixels format)
data_dir = Path("/data/recording/session_001")
recording = si.read_spikeglx(data_dir, stream_name="imec0.ap")

print(f"Probe type:       {recording.get_probe().name}")
print(f"Channels:         {recording.get_num_channels()}")
print(f"Sampling rate:    {recording.get_sampling_frequency()} Hz")
print(f"Duration:         {recording.get_total_duration():.1f} s")
print(f"Total samples:    {recording.get_total_samples()}")

Step 2: Apply Common Reference and Bandpass Filter

import spikeinterface.preprocessing as spre

# Common median reference (removes common noise across all channels)
recording_cmr = spre.common_reference(recording, reference="global", operator="median")

# Bandpass filter: 300–6000 Hz for spikes
recording_filt = spre.bandpass_filter(recording_cmr, freq_min=300, freq_max=6000)

# Remove bad channels automatically
recording_clean, removed_ids = spre.remove_bad_channels(recording_filt)
print(f"Removed {len(removed_ids)} bad channels: {removed_ids}")
print(f"Clean recording: {recording_clean.get_num_channels()} channels")

Step 3: Run Spike Sorting

import spikeinterface.sorters as ss
from pathlib import Path

output_dir = Path("./sorting_output")

# Kilosort4 (recommended for Neuropixels; requires GPU)
sorting = ss.run_sorter(
    "kilosort4",
    recording_clean,
    output_folder=output_dir / "kilosort4",
    remove_existing_folder=True,
    verbose=True,
    # Kilosort4 parameters
    nblocks=5,          # number of drift correction blocks
    Th_learned=8,       # threshold for learned templates
    do_correction=True, # drift correction
)

print(f"Units found: {len(sorting.get_unit_ids())}")
print(f"Spike counts (first 5): {[len(sorting.get_unit_spike_train(u, segment_index=0)) for u in sorting.unit_ids[:5]]}")

Step 4: Compute Waveforms and Quality Metrics

import spikeinterface.full as si
import spikeinterface.qualitymetrics as sqm

# Extract waveforms (snippets around each spike)
waveforms = si.extract_waveforms(
    recording_clean,
    sorting,
    folder="./waveforms",
    ms_before=1.0,      # ms before spike peak
    ms_after=2.0,       # ms after spike peak
    max_spikes_per_unit=1000,
    overwrite=True,
    n_jobs=4,
)

print(f"Waveform shape per unit: {waveforms.get_waveforms(waveforms.unit_ids[0]).shape}")
# (n_spikes, n_samples, n_channels)

# Compute quality metrics
metrics = sqm.compute_quality_metrics(
    waveforms,
    metric_names=["snr", "isi_violation", "firing_rate", "presence_ratio",
                  "amplitude_cutoff", "nearest_neighbor"],
)
print(f"\nQuality metrics summary:")
print(metrics.describe())

Step 5: Curate Units

import pandas as pd

# Curation thresholds (Allen Brain Institute defaults)
thresholds = {
    "snr":                (5.0, None),   # SNR ≥ 5
    "isi_violations_ratio": (None, 0.1), # ISI violation ratio ≤ 10%
    "firing_rate":        (0.1, None),   # firing rate ≥ 0.1 Hz
    "presence_ratio":     (0.9, None),   # present ≥ 90% of recording
    "amplitude_cutoff":   (None, 0.1),   # amplitude cutoff ≤ 10%
}

def apply_thresholds(metrics_df, thresholds):
    mask = pd.Series(True, index=metrics_df.index)
    for metric, (low, high) in thresholds.items():
        if metric not in metrics_df.columns:
            continue
        if low is not None:
            mask &= metrics_df[metric] >= low
        if high is not None:
            mask &= metrics_df[metric] <= high
    return mask

good_units_mask = apply_thresholds(metrics, thresholds)
good_unit_ids = metrics[good_units_mask].index.tolist()

print(f"Total units:   {len(metrics)}")
print(f"Good units:    {len(good_unit_ids)} ({100*len(good_unit_ids)/len(metrics):.0f}%)")

# Filter sorting to good units only
sorting_curated = sorting.select_units(good_unit_ids)

Step 6: Compute PSTHs and Visualize

import numpy as np
import matplotlib.pyplot as plt

def compute_psth(spike_times, event_times, window=(-0.5, 1.0), bin_size=0.01, fs=30000):
    """Compute peri-stimulus time histogram for one unit."""
    bins = np.arange(window[0], window[1] + bin_size, bin_size)
    spike_times_s = spike_times / fs  # samples → seconds
    counts = np.zeros(len(bins) - 1)
    for t_event in event_times:
        rel_times = spike_times_s - t_event
        in_window = rel_times[(rel_times >= window[0]) & (rel_times < window[1])]
        counts += np.histogram(in_window, bins=bins)[0]
    rate = counts / (len(event_times) * bin_size)  # convert to Hz
    return bins[:-1] + bin_size / 2, rate  # bin centers, firing rate

# Example: visual stimulus events at 1.0, 2.5, 4.0, 5.5 s
fs = 30000
event_times_s = np.array([1.0, 2.5, 4.0, 5.5, 7.0, 8.5])

# Plot PSTH for first 4 good units
fig, axes = plt.subplots(2, 2, figsize=(10, 6))
for ax, unit_id in zip(axes.flat, good_unit_ids[:4]):
    spikes = sorting_curated.get_unit_spike_train(unit_id, segment_index=0)
    times, rate = compute_psth(spikes, event_times_s, fs=fs)
    ax.bar(times, rate, width=0.01, color="steelblue", alpha=0.8)
    ax.axvline(0, color="red", lw=1.5, linestyle="--", label="Stimulus")
    ax.set_xlabel("Time from stimulus (s)")
    ax.set_ylabel("Firing rate (Hz)")
    ax.set_title(f"Unit {unit_id}")

plt.tight_layout()
plt.savefig("psth_grid.pdf", bbox_inches="tight")
print("Saved psth_grid.pdf")

Step 7: Export to NWB

import spikeinterface.exporters as sexp

# Export sorted data to Neurodata Without Borders format
nwb_path = "./recording_sorted.nwb"
sexp.export_to_nwb(
    sorting_curated,
    nwb_file_path=nwb_path,
    overwrite=True,
)
print(f"Exported to NWB: {nwb_path}")

# Also export waveforms for Phy manual curation
phy_dir = "./phy_export"
sexp.export_to_phy(
    waveforms,
    output_folder=phy_dir,
    compute_pc_features=True,
    copy_binary=True,
)
print(f"Phy export ready at: {phy_dir}")
print("Launch with: phy template-gui phy_export/params.py")

Key Parameters

Parameter	Module/Function	Default	Range / Options	Effect
freq_min / freq_max	bandpass_filter	300/6000 Hz	150–500 / 3000–10000	Spike band; NP 1.0 standard is 300–6000 Hz
nblocks	Kilosort4	5	0–10	Number of drift correction blocks; 0 disables drift correction
Th_learned	Kilosort4	8	6–12	Detection threshold (× noise level); lower = more spikes, more noise
ms_before / ms_after	extract_waveforms	1.0/2.0	0.5–2.0/1.0–3.0 ms	Waveform snippet window around spike peak
max_spikes_per_unit	extract_waveforms	500	100–5000	Maximum spikes per unit for waveform extraction
snr threshold	quality metrics	—	5–10	Signal-to-noise threshold for unit acceptance
isi_violations_ratio	quality metrics	—	0.05–0.2	Refractory period violation rate; <0.1 is well-isolated
presence_ratio	quality metrics	—	0.9	Fraction of recording where unit is active
bin_size	PSTH	0.01 s	0.001–0.05 s	PSTH temporal resolution; smaller = more detail, noisier

Key Concepts

Spike Sorting Pipeline

Raw voltage → preprocessing (common reference, bandpass) → detection (threshold crossing or learned templates) → clustering (PCA + k-means or Gaussian mixture) → template matching → quality metrics → curation. Kilosort4 adds drift correction, which is critical for chronic NP recordings (tip drift of 5–50 µm over hours degrades unit isolation).

Quality Metrics

• SNR: peak waveform amplitude / noise level. SNR >5 indicates well-isolated unit
• ISI violation ratio: fraction of inter-spike intervals shorter than the refractory period (~1.5 ms). Ratio <0.1 indicates single-unit isolation
• Presence ratio: fraction of recording epochs where unit fired at least one spike. <0.9 suggests unit disappeared or was lost
• Amplitude cutoff: fraction of spikes missing due to detection threshold. <0.1 ensures near-complete detection

Common Recipes

Recipe: Compare Two Sorters on Same Recording

import spikeinterface.sorters as ss
import spikeinterface.comparison as sc

# Run two sorters
sorting_ks4 = ss.run_sorter("kilosort4", recording_clean, output_folder="./ks4")
sorting_sc   = ss.run_sorter("spykingcircus2", recording_clean, output_folder="./sc2")

# Compare outputs
comparison = sc.compare_two_sorters(sorting_ks4, sorting_sc,
                                     sorting1_name="Kilosort4",
                                     sorting2_name="SpykingCircus2")
print(comparison.get_performance())
# Shows: agreement fraction, recall, precision per matched unit pair

Recipe: Population Firing Rate Heatmap

import numpy as np
import matplotlib.pyplot as plt

fs = 30000
duration_s = sorting_curated.get_total_duration()
bin_edges = np.arange(0, duration_s, 0.05)  # 50 ms bins

# Build firing rate matrix: (n_units, n_bins)
fr_matrix = np.zeros((len(good_unit_ids), len(bin_edges)-1))
for i, uid in enumerate(good_unit_ids[:50]):
    spikes_s = sorting_curated.get_unit_spike_train(uid, segment_index=0) / fs
    counts, _ = np.histogram(spikes_s, bins=bin_edges)
    fr_matrix[i] = counts / 0.05  # Hz

# Normalize each unit
fr_norm = (fr_matrix - fr_matrix.mean(1, keepdims=True)) / (fr_matrix.std(1, keepdims=True) + 1e-6)

fig, ax = plt.subplots(figsize=(12, 5))
im = ax.imshow(fr_norm, aspect="auto", cmap="RdBu_r",
               extent=[0, duration_s, len(good_unit_ids[:50]), 0], vmin=-2, vmax=2)
ax.set_xlabel("Time (s)")
ax.set_ylabel("Unit #")
ax.set_title("Population Activity Heatmap (z-scored FR)")
plt.colorbar(im, ax=ax, label="z-score")
plt.tight_layout()
plt.savefig("population_heatmap.pdf", bbox_inches="tight")

Expected Outputs

Output	Format	Typical Content
sorting/	SpikeInterface folder	Spike times per unit; template waveforms
waveforms/	SpikeInterface folder	Waveform snippets (n_spikes, n_samples, n_channels)
quality_metrics.csv	CSV	SNR, ISI violations, firing rate, presence ratio per unit
psth_grid.pdf	PDF	PSTH plots for curated units
recording_sorted.nwb	NWB/HDF5	Portable spike-sorted data for sharing
phy_export/	Phy format	.npy + params.py for manual curation GUI

Troubleshooting

Problem	Cause	Solution
Kilosort GPU memory error	Recording too long or too many channels for VRAM	Process recording in time chunks using si.SubRecording; use NP 2.0 (192 ch) settings
Zero units found	Threshold too high or preprocessing removed all signal	Lower Th_learned to 6; verify recording_clean has non-zero channel data
Excessive ISI violations (>50%)	Multi-unit activity merged as single unit	Manual curation with Phy; increase Th_learned to be more conservative
Waveform extraction OOM	Too many spikes × channels × samples	Reduce max_spikes_per_unit; increase n_jobs for parallel extraction
Drift correction fails	Too few spikes or very short recording	Set nblocks=1 (minimal correction) or nblocks=0 (disable)
NWB export fails	Missing session metadata (subject, date)	Provide NWBFile metadata; or use sexp.export_to_nwb(..., metadata={...})
SpikeGLX file not found	Wrong stream name	List streams: si.get_neo_streams("spikeglx", data_dir)

References

• SpikeInterface documentation — full API, tutorials, and sorter comparison guides
• Kilosort4 paper: Pachitariu et al. (2024), Nature Methods — drift correction and template learning
• SpikeInterface paper: Buccino et al. (2020), eLife — unified framework for extracellular electrophysiology
• ProbeInterface documentation — probe geometry and channel map handling
• Neuropixels documentation — hardware specs, imec reference designs
• NWB documentation — neurophysiology data standard for archiving and sharing