Journal article
DREDge: robust motion correction for high-density extracellular recordings across species
Nature methods, Vol.22(4), pp.788-800
04/2025
DOI: 10.1038/s41592-025-02614-5
PMCID: PMC13055889
PMID: 40050699
Abstract
High-density microelectrode arrays have opened new possibilities for systems neuroscience, but brain motion relative to the array poses challenges for downstream analyses. We introduce DREDge (Decentralized Registration of Electrophysiology Data), a robust algorithm for the registration of noisy, nonstationary extracellular electrophysiology recordings. In addition to estimating motion from action potential data, DREDge enables automated, high-temporal-resolution motion tracking in local field potential data. In human intraoperative recordings, DREDge's local field potential-based tracking reliably recovered evoked potentials and single-unit spike sorting. In recordings of deep probe insertions in nonhuman primates, DREDge tracked motion across centimeters of tissue and several brain regions while mapping single-unit electrophysiological features. DREDge reliably improved motion correction in acute mouse recordings, especially in those made with a recent ultrahigh-density probe. Applying DREDge to recordings from chronic implantations in mice yielded stable motion tracking despite changes in neural activity between experimental sessions. These advances enable automated, scalable registration of electrophysiological data across species, probes and drift types, providing a foundation for downstream analyses of these rich datasets.High-density microelectrode arrays have opened new possibilities for systems neuroscience, but brain motion relative to the array poses challenges for downstream analyses. We introduce DREDge (Decentralized Registration of Electrophysiology Data), a robust algorithm for the registration of noisy, nonstationary extracellular electrophysiology recordings. In addition to estimating motion from action potential data, DREDge enables automated, high-temporal-resolution motion tracking in local field potential data. In human intraoperative recordings, DREDge's local field potential-based tracking reliably recovered evoked potentials and single-unit spike sorting. In recordings of deep probe insertions in nonhuman primates, DREDge tracked motion across centimeters of tissue and several brain regions while mapping single-unit electrophysiological features. DREDge reliably improved motion correction in acute mouse recordings, especially in those made with a recent ultrahigh-density probe. Applying DREDge to recordings from chronic implantations in mice yielded stable motion tracking despite changes in neural activity between experimental sessions. These advances enable automated, scalable registration of electrophysiological data across species, probes and drift types, providing a foundation for downstream analyses of these rich datasets.
Details
- Title: Subtitle
- DREDge: robust motion correction for high-density extracellular recordings across species
- Creators
- Charlie Windolf - Columbia UniversityHan Yu - Columbia UniversityAngelique C Paulk - Harvard UniversityDomokos Meszéna - Harvard UniversitySamuel Garcia - Centre de Recherche en Neurosciences de LyonWilliam Muñoz - Massachusetts General HospitalBrian Coughlin - Harvard UniversityJulien Boussard - Columbia UniversityMargot Elmaleh - NYU Langone HealthRichard Hardstone - Harvard UniversityDavid Christianson - University of Iowa Hospitals and ClinicsIrene Caprara - Massachusetts General HospitalJeremy D W Greenlee - University of IowaMohsen Jamali - Massachusetts General HospitalCsaba Horváth - Institute of Cognitive Neuroscience and PsychologyYoav Kfir - Massachusetts General HospitalRichárd Fiáth - Institute of Cognitive Neuroscience and PsychologyDuo Xu - University of California, San FranciscoIstván Ulbert - Institute of Cognitive Neuroscience and PsychologyJason E Chung - University of California, San FranciscoMichael A Long - NYU Langone HealthJ Anthony Movshon - New York UniversityZhiwen Ye - University of WashingtonMichael N Shadlen - Columbia UniversityJordan Shaker - University of WashingtonMark M Churchland - Columbia UniversityAnna Lebedeva - University College LondonAnne K Churchland - University of California, Los AngelesR T Raghavan - New York UniversityNicholas A Steinmetz - University of WashingtonEric Trautmann - Columbia UniversityEdward F Chang - University of California, San FranciscoMax Melin - University of California, Los AngelesJeffrey S Schweitzer - Massachusetts General HospitalJoão Couto - University of California, Los AngelesZiv M Williams - Massachusetts General HospitalSydney S Cash - Massachusetts General HospitalLiam Paninski - Columbia UniversityErdem Varol - New York University
- Resource Type
- Journal article
- Publication Details
- Nature methods, Vol.22(4), pp.788-800
- DOI
- 10.1038/s41592-025-02614-5
- PMID
- 40050699
- PMCID
- PMC13055889
- NLM abbreviation
- Nat Methods
- ISSN
- 1548-7105
- eISSN
- 1548-7105
- Publisher
- NATURE PORTFOLIO; BERLIN
- Grant note
- ECORTiny Blue Dot FoundationNational Institutes of Health (NIH)Howard Hughes Medical Institute at Stanford UniversityGrossman centerBrain and Behavior Research FoundationSimons Foundation: 344 543023 NSF Neuronex: DBI-1707398 Gatsby Charitable FoundationPew Biomedical Scholars ProgramHungarian Brain Research Program GrantKlingenstein-Simons Fellowship in Neuroscience: PD143582 OTKA HungarianNIH Neuroscience Resident Research Program: R25NS065743 Simons Collaboration on the Global BrainNIH: R01 DC019354 CZI FoundationNIH BRAIN Initiative: U01NS113252
We thank Y. Chou, D. Soper, A. Tripp, F. Minidio, A. Zhang, A. O'Donnell and M. Okun for their help in data collection. We especially thank the patients for participating in this research. We thank M. Carandini, J. Colonell, O. Winter, A. Zimnik and the IBL for helpful discussions and data coordination. We thank A. Buccino, G. Chapuis, S. Garcia and P. Yger, and also the Simons Collaboration on the Global Brain Spike Sorting Working group for many useful discussions. We also thank M. Voeroeslakos and G. Buzsaki (NYU Grossman School of Medicine) for helpful feedback and additional test datasets not analyzed here. This research was supported by the ECOR and K24-NS088568 (to S.S.C.) and the Tiny Blue Dot Foundation (to S.S.C. and A.C.P.) and National Institutes of Health (NIH) grant U01NS121616 (to Z.M.W.). This research was also supported by the Howard Hughes Medical Institute at Stanford University (to E.M.T.). E.M.T. is supported by the Grossman center and the Brain and Behavior Research Foundation. C.W., H.Y., J.B., E.V. and L.P. are funded by Simons Foundation grant 344 543023, NSF Neuronex Award DBI-1707398 and the Gatsby Charitable Foundation. E.V. is also supported by R00MH128772. The rat brain in vivo data have been recorded within the Hungarian Brain Research Program Grant (NAP2022-I-2/2022). D.M. is also supported by the OTKA Hungarian postdoctoral grant (PD143582). W.M. is supported by the NIH Neuroscience Resident Research Program R25NS065743. This research was also supported by the Simons Collaboration on the Global Brain and NIH R01 DC019354 (to M.A.L.). E.F.C. is supported by the CZI Foundation. Z.Y., J.S. and N.A.S. were supported by the NIH BRAIN Initiative (U01NS113252), the Pew Biomedical Scholars Program and the Klingenstein-Simons Fellowship in Neuroscience. The views and conclusions contained in this paper are those of the authors and do not represent the official policies, either expressed or implied, of the funding sources. The funders had no role in the study design, data collection, analysis, decision to publish, or preparation of the manuscript.
- Language
- English
- Electronic publication date
- 03/06/2025
- Date published
- 04/2025
- Academic Unit
- Stead Family Department of Pediatrics; Iowa Neuroscience Institute; Neurosurgery; Otolaryngology
- Record Identifier
- 9984798223902771
Metrics
6 Record Views