claude-scientific-skills/scientific-skills/neuropixels-analysis/MOTION_CORRECTION.md

Motion/Drift Correction Reference

Mechanical drift during acute probe insertion is a major challenge for Neuropixels recordings. This guide covers detection, estimation, and correction of motion artifacts.

Why Motion Correction Matters

• Neuropixels probes can drift 10-100+ μm during recording
• Uncorrected drift leads to:
  • Units appearing/disappearing mid-recording
  • Waveform amplitude changes
  • Incorrect spike-unit assignments
  • Reduced unit yield

Detection: Check Before Sorting

Always visualize drift before running spike sorting!

import spikeinterface.full as si
from spikeinterface.sortingcomponents.peak_detection import detect_peaks
from spikeinterface.sortingcomponents.peak_localization import localize_peaks

# Preprocess first (don't whiten - affects peak localization)
rec = si.highpass_filter(recording, freq_min=400.)
rec = si.common_reference(rec, operator='median', reference='global')

# Detect 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.,
    n_jobs=8,
    chunk_duration='1s',
    progress_bar=True
)

# Localize peaks
peak_locations = localize_peaks(
    rec, peaks,
    method='center_of_mass',
    n_jobs=8,
    chunk_duration='1s'
)

# Visualize drift
si.plot_drift_raster_map(
    peaks=peaks,
    peak_locations=peak_locations,
    recording=rec,
    clim=(-200, 0)  # Adjust color limits
)

Interpreting Drift Plots

Pattern	Interpretation	Action
Horizontal bands, stable	No significant drift	Skip correction
Diagonal bands (slow)	Gradual settling drift	Use motion correction
Rapid jumps	Brain pulsation or movement	Use non-rigid correction
Chaotic patterns	Severe instability	Consider discarding segment

Motion Correction Methods

Quick Correction (Recommended Start)

# Simple one-liner with preset
rec_corrected = si.correct_motion(
    recording=rec,
    preset='nonrigid_fast_and_accurate'
)

Available Presets

Preset	Speed	Accuracy	Best For
rigid_fast	Fast	Low	Quick check, small drift
kilosort_like	Medium	Good	Kilosort-compatible results
nonrigid_accurate	Slow	High	Publication-quality
nonrigid_fast_and_accurate	Medium	High	Recommended default
dredge	Slow	Highest	Best results, complex drift
dredge_fast	Medium	High	DREDge with less compute

Full Control Pipeline

from spikeinterface.sortingcomponents.motion import (
    estimate_motion,
    interpolate_motion
)

# Step 1: Estimate motion
motion, temporal_bins, spatial_bins = estimate_motion(
    rec,
    peaks,
    peak_locations,
    method='decentralized',
    direction='y',
    rigid=False,          # Non-rigid for Neuropixels
    win_step_um=50,       # Spatial window step
    win_sigma_um=150,     # Spatial smoothing
    bin_s=2.0,            # Temporal bin size
    progress_bar=True
)

# Step 2: Visualize motion estimate
si.plot_motion(
    motion,
    temporal_bins,
    spatial_bins,
    recording=rec
)

# Step 3: Apply correction via interpolation
rec_corrected = interpolate_motion(
    recording=rec,
    motion=motion,
    temporal_bins=temporal_bins,
    spatial_bins=spatial_bins,
    border_mode='force_extrapolate'
)

Save Motion Estimate

# Save for later use
import numpy as np
np.savez('motion_estimate.npz',
         motion=motion,
         temporal_bins=temporal_bins,
         spatial_bins=spatial_bins)

# Load later
data = np.load('motion_estimate.npz')
motion = data['motion']
temporal_bins = data['temporal_bins']
spatial_bins = data['spatial_bins']

DREDge: State-of-the-Art Method

DREDge (Decentralized Registration of Electrophysiology Data) is currently the best-performing motion correction method.

Using DREDge Preset

# AP-band motion estimation
rec_corrected = si.correct_motion(rec, preset='dredge')

# Or compute explicitly
motion, motion_info = si.compute_motion(
    rec,
    preset='dredge',
    output_motion_info=True,
    folder='motion_output/',
    **job_kwargs
)

LFP-Based Motion Estimation

For very fast drift or when AP-band estimation fails:

# Load LFP stream
lfp = si.read_spikeglx('/path/to/data', stream_name='imec0.lf')

# Estimate motion from LFP (faster, handles rapid drift)
motion_lfp, motion_info = si.compute_motion(
    lfp,
    preset='dredge_lfp',
    output_motion_info=True
)

# Apply to AP recording
rec_corrected = interpolate_motion(
    recording=rec,  # AP recording
    motion=motion_lfp,
    temporal_bins=motion_info['temporal_bins'],
    spatial_bins=motion_info['spatial_bins']
)

Integration with Spike Sorting

Option 1: Pre-correction (Recommended)

# Correct before sorting
rec_corrected = si.correct_motion(rec, preset='nonrigid_fast_and_accurate')

# Save corrected recording
rec_corrected = rec_corrected.save(folder='preprocessed_motion_corrected/',
                                    format='binary', n_jobs=8)

# Run spike sorting on corrected data
sorting = si.run_sorter('kilosort4', rec_corrected, output_folder='ks4/')

Option 2: Let Kilosort Handle It

Kilosort 2.5+ has built-in drift correction:

sorting = si.run_sorter(
    'kilosort4',
    rec,  # Not motion corrected
    output_folder='ks4/',
    nblocks=5,  # Non-rigid blocks for drift correction
    do_correction=True  # Enable Kilosort's drift correction
)

Option 3: Post-hoc Correction

# Sort first
sorting = si.run_sorter('kilosort4', rec, output_folder='ks4/')

# Then estimate motion from sorted spikes
# (More accurate as it uses actual spike times)
from spikeinterface.sortingcomponents.motion import estimate_motion_from_sorting

motion = estimate_motion_from_sorting(sorting, rec)

Parameters Deep Dive

Peak Detection

peaks = detect_peaks(
    rec,
    method='locally_exclusive',  # Best for dense probes
    noise_levels=noise_levels,
    detect_threshold=5,          # Lower = more peaks (noisier estimate)
    radius_um=50.,               # Exclusion radius
    exclude_sweep_ms=0.1,        # Temporal exclusion
)

Motion Estimation

motion = estimate_motion(
    rec, peaks, peak_locations,
    method='decentralized',      # 'decentralized' or 'iterative_template'
    direction='y',               # Along probe axis
    rigid=False,                 # False for non-rigid
    bin_s=2.0,                   # Temporal resolution (seconds)
    win_step_um=50,              # Spatial window step
    win_sigma_um=150,            # Spatial smoothing sigma
    margin_um=0,                 # Margin at probe edges
    win_scale_um=150,            # Window scale for weights
)

Troubleshooting

Over-correction (Wavy Patterns)

# Increase temporal smoothing
motion = estimate_motion(..., bin_s=5.0)  # Larger bins

# Or use rigid correction for small drift
motion = estimate_motion(..., rigid=True)

Under-correction (Drift Remains)

# Decrease spatial window for finer non-rigid estimate
motion = estimate_motion(..., win_step_um=25, win_sigma_um=75)

# Use more peaks
peaks = detect_peaks(..., detect_threshold=4)  # Lower threshold

Edge Artifacts

rec_corrected = interpolate_motion(
    rec, motion, temporal_bins, spatial_bins,
    border_mode='force_extrapolate',  # or 'remove_channels'
    spatial_interpolation_method='kriging'
)

Validation

After correction, re-visualize to confirm:

# Re-detect peaks on corrected recording
peaks_corrected = detect_peaks(rec_corrected, ...)
peak_locations_corrected = localize_peaks(rec_corrected, peaks_corrected, ...)

# Plot before/after comparison
fig, axes = plt.subplots(1, 2, figsize=(14, 6))

# Before
si.plot_drift_raster_map(peaks, peak_locations, rec, ax=axes[0])
axes[0].set_title('Before Correction')

# After
si.plot_drift_raster_map(peaks_corrected, peak_locations_corrected,
                         rec_corrected, ax=axes[1])
axes[1].set_title('After Correction')

References

• SpikeInterface Motion Correction Docs
• Handle Drift Tutorial
• DREDge GitHub
• Windolf et al. (2023) "DREDge: robust motion correction for high-density extracellular recordings"