DREDge: robust motion correction for high-density extracellular recordings across species

Abstract

High-density microelectrode arrays (MEAs) have opened new possibilities for systems neuroscience in human and non-human animals, but brain tissue motion relative to the array poses a challenge for downstream analyses, particularly in human recordings. We introduce DREDge (Decentralized Registration of Electrophysiology Data), a robust algorithm which is well suited for the registration of noisy, nonstationary extracellular electrophysiology recordings. In addition to estimating motion from spikes in the action potential (AP) frequency band, DREDge enables automated tracking of motion at high temporal resolution in the local field potential (LFP) frequency band. In human intraoperative recordings, which often feature fast (period <1s) motion, DREDge correction in the LFP band enabled reliable recovery of evoked potentials, and significantly reduced single-unit spike shape variability and spike sorting error. Applying DREDge to recordings made during deep probe insertions in nonhuman primates demonstrated the possibility of tracking probe motion of centimeters across several brain regions while simultaneously mapping single unit electrophysiological features. DREDge reliably delivered improved motion correction in acute mouse recordings, especially in those made with an recent ultra-high density probe. We also implemented a procedure for applying DREDge to recordings made across tens of days in chronic implantations in mice, reliably yielding stable motion tracking despite changes in neural activity across experimental sessions. Together, these advances enable automated, scalable registration of electrophysiological data across multiple species, probe types, and drift cases, providing a stable foundation for downstream scientific analyses of these rich datasets.

Large scale, simultaneous, chronic neural recordings from multiple brain areas

“…We reasoned that a condition where the mouse is locomoting vigorously and the skull is fixed would be more likely to produce large artifacts than in a freely moving configuration. We deployed DREDge (Windolf et al, 2023), a motion registration algorithm for electrophysiological data that has been extensively validated in similar recordings with imposed motion, to quantify motion on a single probe, with shanks in cortical and thalamic structures. We chose a superficial and a deep target because it is possible that motion affects different structures differently and wanted to investigate how stable the use of silicone adhesive is at reducing motion of tissue close to the craniotomy.…”

“…Interestingly, movement was more prevalent for the first month, suggesting that it might be related to recovery from surgery. This magnitude of motion can be easily corrected with registration algorithms and is less than the motion observed within acute sessions, in the most extreme cases (Windolf et al, 2023).…”

“…Sessions were spike-sorted with Kilosort4.0 (Pachitariu et al, 2023) using default parameters. To compute motion estimates using DREDGe (Windolf et al, 2023), we performed spike detection and localization with SpikeInterface (Buccino et al, 2020). Data aggregation and management were performed with DataJoint (Yatsenko et al, 2015).…”

“…The median shift between sessions was restricted to less than the size of one recording site (4.9±7.6 µm for thalamus and 1.6±8.2µm median ± std), suggesting that comparisons across sessions are not likely to be affected by motion of the tissue in relation to the probe. This magnitude of motion can be easily corrected with registration algorithms and is less than the motion observed within acute sessions, in the most extreme cases (Windolf et al, 2023). The electrodes in chronic recordings can remain implanted for months and therefore can evoke inflammatory responses that in turn encapsulate the electrodes and impact single unit yield.…”