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

Charlie Windolf^{1

2}, Han Yu^{3

4}, Angelique C Paulk⁵, Domokos Meszéna^{5

6}, William Muñoz⁷, Julien Boussard^{8

3}, Richard Hardstone⁵, Irene Caprara⁷, Mohsen Jamali⁷, Yoav Kfir⁷, Duo Xu^{9

10}, Jason E Chung¹⁰, Kristin K Sellers^{9

10}, Zhiwen Ye¹¹, Jordan Shaker¹¹, Anna Lebedeva¹², R T Raghavan¹³, Eric Trautmann^{3

14

15

16

17}, Max Melin¹⁸, João Couto¹⁸, Samuel Garcia¹⁹, Brian Coughlin⁵, Margot Elmaleh²⁰, David Christianson²¹, Jeremy D W Greenlee²¹, Csaba Horváth⁶, Richárd Fiáth⁶, István Ulbert^{6

22

23}, Michael A Long²⁰, J Anthony Movshon¹³, Michael N Shadlen^{3

24}, Mark M Churchland^{3

14

15

25}, Anne K Churchland¹⁸, Nicholas A Steinmetz¹¹, Edward F Chang^{9

10}, Jeffrey S Schweitzer⁷, Ziv M Williams⁷, Sydney S Cash⁵, Liam Paninski^{8

3

14

15}, Erdem Varol^{8

3

26}

Affiliations

¹ Department of Statistics, Columbia University, New York City, NY, USA. ciw2107@columbia.edu.
² Zuckerman Institute, Columbia University, New York City, NY, USA. ciw2107@columbia.edu.
³ Zuckerman Institute, Columbia University, New York City, NY, USA.
⁴ Department of Electrical Engineering, Columbia University, New York City, NY, USA.
⁵ Department of Neurology, Center for Neurotechnology and Neurorecovery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
⁶ Institute of Cognitive Neuroscience and Psychology, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
⁷ Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
⁸ Department of Statistics, Columbia University, New York City, NY, USA.
⁹ Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
¹⁰ Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
¹¹ Department of Neurobiology and Biophysics, University of Washington, Seattle, WA, USA.
¹² Cortexlab, University College London, London, UK.
¹³ Center for Neural Science, New York University, New York City, NY, USA.
¹⁴ Department of Neuroscience, Columbia University Medical Center, New York City, NY, USA.
¹⁵ Grossman Center for the Statistics of Mind, Columbia University, New York City, NY, USA.
¹⁶ CTRL-Labs at Reality Labs, Seattle, WA, USA.
¹⁷ Department of Neurological Surgery, University of California, Davis, Davis, CA, USA.
¹⁸ David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
¹⁹ Centre National de la Recherche Scientifique, Centre de Recherche en Neurosciences de Lyon, Lyon, France.
²⁰ NYU Neuroscience Institute and Department of Otolaryngology, New York University Langone Medical Center, New York City, NY, US.
²¹ Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA.
²² Department of Information Technology and Bionics, Péter Pázmány Catholic University, Budapest, Hungary.
²³ Department of Neurosurgery and Neurointervention, Faculty of Medicine, Semmelweis University, Budapest, Hungary.
²⁴ Howard Hughes Medical Institute, Chevy Chase, MD, USA.
²⁵ Kavli Institute for Brain Science, Columbia University, New York City, NY, USA.
²⁶ Department of Computer Science & Engineering, New York University, New York City, NY, USA.

PMID: 40050699
DOI: 10.1038/s41592-025-02614-5

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

Charlie Windolf et al. Nat Methods. 2025 Apr.

. 2025 Apr;22(4):788-800.

doi: 10.1038/s41592-025-02614-5. Epub 2025 Mar 6.

Authors

Affiliations

¹ Department of Statistics, Columbia University, New York City, NY, USA. ciw2107@columbia.edu.
² Zuckerman Institute, Columbia University, New York City, NY, USA. ciw2107@columbia.edu.
³ Zuckerman Institute, Columbia University, New York City, NY, USA.
⁴ Department of Electrical Engineering, Columbia University, New York City, NY, USA.
⁵ Department of Neurology, Center for Neurotechnology and Neurorecovery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
⁶ Institute of Cognitive Neuroscience and Psychology, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
⁷ Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
⁸ Department of Statistics, Columbia University, New York City, NY, USA.
⁹ Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
¹⁰ Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
¹¹ Department of Neurobiology and Biophysics, University of Washington, Seattle, WA, USA.
¹² Cortexlab, University College London, London, UK.
¹³ Center for Neural Science, New York University, New York City, NY, USA.
¹⁴ Department of Neuroscience, Columbia University Medical Center, New York City, NY, USA.
¹⁵ Grossman Center for the Statistics of Mind, Columbia University, New York City, NY, USA.
¹⁶ CTRL-Labs at Reality Labs, Seattle, WA, USA.
¹⁷ Department of Neurological Surgery, University of California, Davis, Davis, CA, USA.
¹⁸ David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
¹⁹ Centre National de la Recherche Scientifique, Centre de Recherche en Neurosciences de Lyon, Lyon, France.
²⁰ NYU Neuroscience Institute and Department of Otolaryngology, New York University Langone Medical Center, New York City, NY, US.
²¹ Department of Neurosurgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA.
²² Department of Information Technology and Bionics, Péter Pázmány Catholic University, Budapest, Hungary.
²³ Department of Neurosurgery and Neurointervention, Faculty of Medicine, Semmelweis University, Budapest, Hungary.
²⁴ Howard Hughes Medical Institute, Chevy Chase, MD, USA.
²⁵ Kavli Institute for Brain Science, Columbia University, New York City, NY, USA.
²⁶ Department of Computer Science & Engineering, New York University, New York City, NY, USA.

PMID: 40050699
DOI: 10.1038/s41592-025-02614-5

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.

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Conflict of interest statement

Competing interests: The MGH Translational Research Center has clinical research support agreements with Neuralink, Paradromics and Synchron, for which S.S.C. provides consultative input. E.M.T. works for Meta Platform’s Reality Lab, but the work presented here was performed in E.M.T.’s prior role at Columbia. None of these entities listed are involved with this research or the NP device. The remaining authors declare no competing interests.

Update of

DREDge: robust motion correction for high-density extracellular recordings across species.
Windolf C, Yu H, Paulk AC, Meszéna D, Muñoz W, Boussard J, Hardstone R, Caprara I, Jamali M, Kfir Y, Xu D, Chung JE, Sellers KK, Ye Z, Shaker J, Lebedeva A, Raghavan M, Trautmann E, Melin M, Couto J, Garcia S, Coughlin B, Horváth C, Fiáth R, Ulbert I, Movshon JA, Shadlen MN, Churchland MM, Churchland AK, Steinmetz NA, Chang EF, Schweitzer JS, Williams ZM, Cash SS, Paninski L, Varol E. Windolf C, et al. bioRxiv [Preprint]. 2023 Oct 29:2023.10.24.563768. doi: 10.1101/2023.10.24.563768. bioRxiv. 2023. Update in: Nat Methods. 2025 Apr;22(4):788-800. doi: 10.1038/s41592-025-02614-5. PMID: 37961359 Free PMC article. Updated. Preprint.

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

Update of

References

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources