Abstract

Sensory, motor and cognitive operations involve the coordinated action of large neuronal populations across multiple brain regions in both superficial and deep structures1,2. Existing extracellular probes record neural activity with excellent spatial and temporal (sub-millisecond) resolution, but from only a few dozen neurons per shank. Optical Ca2+ imaging3,4,5 offers more coverage but lacks the temporal resolution needed to distinguish individual spikes reliably and does not measure local field potentials. Until now, no technology compatible with use in unrestrained animals has combined high spatiotemporal resolution with large volume coverage. Here we design, fabricate and test a new silicon probe known as Neuropixels to meet this need. Each probe has 384 recording channels that can programmably address 960 complementary metal–oxide–semiconductor (CMOS) processing-compatible low-impedance TiN6 sites that tile a single 10-mm long, 70 × 20-μm cross-section shank. The 6 × 9-mm probe base is fabricated with the shank on a single chip. Voltage signals are filtered, amplified, multiplexed and digitized on the base, allowing the direct transmission of noise-free digital data from the probe. The combination of dense recording sites and high channel count yielded well-isolated spiking activity from hundreds of neurons per probe implanted in mice and rats. Using two probes, more than 700 well-isolated single neurons were recorded simultaneously from five brain structures in an awake mouse. The fully integrated functionality and small size of Neuropixels probes allowed large populations of neurons from several brain structures to be recorded in freely moving animals. This combination of high-performance electrode technology and scalable chip fabrication methods opens a path towards recording of brain-wide neural activity during behaviour.

  • Subscribe to Nature for full access:

    $199

    Subscribe

Additional access options:

Already a subscriber?  Log in  now or  Register  for online access.

References

  1. 1.

    , & Recording of brain activity across spatial scales. Curr. Opin. Neurobiol. 32, 68–77 (2015)

  2. 2.

    et al. BRAIN 2025: a Scientific Vision; Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Working Group Report to the Advisory Committee to the Director, NIH. Available at: (2014)

  3. 3.

    , , & A large field of view two-photon mesoscope with subcellular resolution for in vivo imaging. eLife 5, e14472 (2016)

  4. 4.

    , , & Cellular level brain imaging in behaving mammals: an engineering approach. Neuron 86, 140–159 (2015)

  5. 5.

    , , , & Whole-brain functional imaging at cellular resolution using light-sheet microscopy. Nat. Methods 10, 413–420 (2013)

  6. 6.

    Titanium nitride electrode. US patent 9,384,990 (2016)

  7. 7.

    Large-scale recording of neuronal ensembles. Nat. Neurosci. 7, 446–451 (2004)

  8. 8.

    & How advances in neural recording affect data analysis. Nat. Neurosci. 14, 139–142 (2011)

  9. 9.

    , , & Synchronous bursts of action potentials in ganglion cells of the developing mammalian retina. Science 252, 939–943 (1991)

  10. 10.

    & Dynamics of the hippocampal ensemble code for space. Science 261, 1055–1058 (1993)

  11. 11.

    , , & State-of-the-art MEMS and microsystem tools for brain research. Microsyst. Nanoeng. 3, 16066 (2017)

  12. 12.

    , , , & Accuracy of tetrode spike separation as determined by simultaneous intracellular and extracellular measurements. J. Neurophysiol. 84, 401–414 (2000)

  13. 13.

    et al. A neural probe with up to 966 electrodes and up to 384 configurable channels in 0.13 μm SOI CMOS. IEEE Trans. Biomed. Circuits Syst. 11, 510–522 (2017)

  14. 14.

    et al. Close-packed silicon microelectrodes for scalable spatially oversampled neural recording. IEEE Trans. Biomed. Eng. 63, 120–130 (2016)

  15. 15.

    , , , & Nanofabricated neural probes for dense 3-D recordings of brain activity. Nano Lett. 16, 6857–6862 (2016)

  16. 16.

    , , , & Brain activity mapping at multiple scales with silicon microprobes containing 1,024 electrodes. J. Neurophysiol. 114, 2043–2052 (2015)

  17. 17.

    et al. Poly(3,4-ethylenedioxythiophene) (PEDOT) polymer coatings facilitate smaller neural recording electrodes. J. Neural Eng. 8, 014001 (2011)

  18. 18.

    et al. Thalamic nuclei convey diverse contextual information to layer 1 of visual cortex. Nat. Neurosci. 19, 299–307 (2016)

  19. 19.

    , , , & Fast and accurate spike sorting of high-channel count probes with KiloSort. Adv. Neural Inf. Process. Syst. 4448–4456 (2016)

  20. 20.

    et al. Spike sorting for large, dense electrode arrays. Nat. Neurosci. 19, 634–641 (2016)

  21. 21.

    , , , & Optogenetics in neural systems. Neuron 71, 9–34 (2011)

  22. 22.

    , , , & Theta sequences are essential for internally generated hippocampal firing fields. Nat. Neurosci. 18, 282–288 (2015)

  23. 23.

    , , , & High-frequency network oscillation in the hippocampus. Science 256, 1025–1027 (1992)

  24. 24.

    et al. Relationship between intracortical electrode design and chronic recording function. Biomaterials 34, 8061–8074 (2013)

  25. 25.

    , , , & Microstructure of a spatial map in the entorhinal cortex. Nature 436, 801–806 (2005)

  26. 26.

    et al. Real-time spike sorting platform for high-density extracellular probes with ground-truth validation and drift correction. Preprint at (2017)

  27. 27.

    Neural signatures of cell assembly organization. Nat. Rev. Neurosci. 6, 399–407 (2005)

  28. 28.

    , , & Techniques for extracting single-trial activity patterns from large-scale neural recordings. Curr. Opin. Neurobiol. 17, 609–618 (2007)

  29. 29.

    et al. The brain activity map project and the challenge of functional connectomics. Neuron 74, 970–974 (2012)

  30. 30.

    et al. Grid cells in pre- and parasubiculum. Nat. Neurosci. 13, 987–994 (2010)

  31. 31.

    et al. Removable cranial windows for long-term imaging in awake mice. Nat. Protocols 9, 2515–2538 (2014)

  32. 32.

    , & Unsupervised spike detection and sorting with wavelets and superparamagnetic clustering. Neural Comput. 16, 1661–1687 (2004)

  33. 33.

    , , & Long term recordings with immobile silicon probes in the mouse cortex. PLoS One 11, e0151180 (2016)

Download references

Acknowledgements

We thank the support of the charities that fully funded this work: Howard Hughes Medical Institute’s Janelia Research Campus, Allen Institute for Brain Science, Gatsby Charitable Foundation (grant GAT3353), and the Wellcome Trust (grant 100154). We thank S. Caddick for early and continued enthusiastic support of the project. We thank G. Buzsáki for advice and D. Rinberg for early discussions and advocacy. C.M., S.L.G. and C.A.A. would like to thank NSG portal personnel for offering core-hour access to the San Diego Supercomputer Center, troubleshooting and support. The Allen Institute for Brain Science wishes to thank the enduring support of our founders, Paul G. Allen and Jody Allen, without whom this work could not have been accomplished. J.C., C.A. and V.B. were funded by NERF. Experiments and software development in the laboratory of M.C. and K.D.H. were supported by the Wellcome Trust (grants 095668 and 095669). M.C. holds the GlaxoSmithKline/Fight for Sight Chair in Visual Neuroscience. N.A.S. was supported by postdoctoral fellowships from the Human Frontier Science Program and the Marie Curie Actions of the EU.

Author information

Author notes

    • James J. Jun
    • , Nicholas A. Steinmetz
    • , Joshua H. Siegle
    • , Daniel J. Denman
    • , Marius Bauza
    • , Brian Barbarits
    •  & Albert K. Lee

    These authors contributed equally to this work.

Affiliations

  1. HHMI Janelia Research Campus, 19700 Helix Drive, Ashburn, Virginia 20147, USA.

    • James J. Jun
    • , Brian Barbarits
    • , Albert K. Lee
    • , Mladen Barbic
    • , Diego A. Gutnisky
    • , Bill Karsh
    • , P. Dylan Rich
    • , Wei-lung Sun
    • , Karel Svoboda
    •  & Timothy D. Harris
  2. UCL Institute of Neurology, University College London, London WC1N 3BG, UK.

    • Nicholas A. Steinmetz
    • , Michael Okun
    • , Marius Pachitariu
    • , Cyrille Rossant
    •  & Kenneth D. Harris
  3. Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6DE, UK.

    • Nicholas A. Steinmetz
    • , Michael Häusser
    • , Michael Okun
    • , Marius Pachitariu
    • , Cyrille Rossant
    •  & Kenneth D. Harris
  4. UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK.

    • Nicholas A. Steinmetz
    •  & Matteo Carandini
  5. Allen Institute for Brain Science, 615 Westlake Avenue North, Seattle, Washington 98109, USA.

    • Joshua H. Siegle
    • , Daniel J. Denman
    • , Costas A. Anastassiou
    • , Timothy J. Blanche
    • , Sergey L. Gratiy
    • , Peter Ledochowitsch
    • , Catalin Mitelut
    •  & Christof Koch
  6. Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK.

    • Marius Bauza
    •  & John O’Keefe
  7. Sainsbury Wellcome Centre, University College London, London W1T 4JG, UK.

    • Marius Bauza
    •  & John O’Keefe
  8. Department of Neurology, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada.

    • Costas A. Anastassiou
    •  & Catalin Mitelut
  9. imec, Kapeldreef 75, 3001 Heverlee, Leuven, Belgium.

    • Alexandru Andrei
    • , Vincent Bonin
    • , Barundeb Dutta
    • , Carolina Mora Lopez
    • , Silke Musa
    •  & Jan Putzeys
  10. Neuro-Electronics Research Flanders, Kapeldreef 75, 3001 Leuven, Belgium.

    • Çağatay Aydın
    • , Vincent Bonin
    •  & João Couto
  11. KU Leuven, Department of Biology, Naamsestraat 59, 3000 Leuven, Belgium.

    • Çağatay Aydın
    • , Vincent Bonin
    •  & João Couto
  12. White Matter LLC, 999 3rd Avenue 700, 98104 Seattle, USA.

    • Timothy J. Blanche
  13. VIB, 3001 Leuven, Belgium.

    • Vincent Bonin
  14. Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, UK.

    • Michael Häusser
  15. Centre for Systems Neuroscience, University of Leicester, Leicester LE1 7QR, UK.

    • Michael Okun

Authors

  1. Search for James J. Jun in:

  2. Search for Nicholas A. Steinmetz in:

  3. Search for Joshua H. Siegle in:

  4. Search for Daniel J. Denman in:

  5. Search for Marius Bauza in:

  6. Search for Brian Barbarits in:

  7. Search for Albert K. Lee in:

  8. Search for Costas A. Anastassiou in:

  9. Search for Alexandru Andrei in:

  10. Search for Çağatay Aydın in:

  11. Search for Mladen Barbic in:

  12. Search for Timothy J. Blanche in:

  13. Search for Vincent Bonin in:

  14. Search for João Couto in:

  15. Search for Barundeb Dutta in:

  16. Search for Sergey L. Gratiy in:

  17. Search for Diego A. Gutnisky in:

  18. Search for Michael Häusser in:

  19. Search for Bill Karsh in:

  20. Search for Peter Ledochowitsch in:

  21. Search for Carolina Mora Lopez in:

  22. Search for Catalin Mitelut in:

  23. Search for Silke Musa in:

  24. Search for Michael Okun in:

  25. Search for Marius Pachitariu in:

  26. Search for Jan Putzeys in:

  27. Search for P. Dylan Rich in:

  28. Search for Cyrille Rossant in:

  29. Search for Wei-lung Sun in:

  30. Search for Karel Svoboda in:

  31. Search for Matteo Carandini in:

  32. Search for Kenneth D. Harris in:

  33. Search for Christof Koch in:

  34. Search for John O’Keefe in:

  35. Search for Timothy D. Harris in:

Contributions

A.K.L., T.D.H. and B.D. conceived and originated the project. T.D.H., C.K., J.O., M.C., K.D.H., M.H., A.K.L. and K.S. secured project funding. T.D.H., A.K.L., B.D., S.M., C.M.L., J.P., J.O., C.K., T.J.B., J.J.J., N.A.S., J.H.S., D.J.D., M.Bau, B.B., D.A.G., K.D.H., M.H., B.K., P.L., P.D.R. and K.S. determined specifications. A.A., C.M.L., S.M., J.P., W.S. and T.D.H. designed and produced devices and firmware. J.J.J., N.A.S., J.H.S., D.J.D., B.B., T.J.B., B.K., P.L., C.M.L., S.M., J.P., W.S. and T.D.H. tested devices in vitro. N.A.S., J.H.S., D.J.D., M.Bar, V.B., C.A. and J.C. performed acute recordings in mouse or rat. J.J.J. and P.D.R. performed chronic recordings in the rat mPFC. M.Bau performed chronic recordings in the rat entorhinal cortex. N.A.S. and M.O. performed chronic recordings in mouse. J.J.J., N.A.S., J.H.S., M.Bau, B.B., T.J.B., C.M.L., S.M., J.P. and W.S. developed instrumentation or other materials. J.J.J., N.A.S., J.H.S., D.J.D., M.Bau, B.B., A.K.L., M.Bar, T.J.B., V.B., M.C., J.C., D.A.G., K.D.H., M.H., P.L., J.O., M.O., P.D.R., K.S. and T.D.H. designed experiments. B.K., J.P., J.H.S., D.J.D., J.J.J., M.P., K.D.H. and C.R. wrote software for data acquisition or analysis. C.A.A., S.L.G. and C.M. performed simulations. J.J.J., N.A.S., J.H.S., D.J.D., M.Bau, B.B., C.A. and J.C. analysed data. T.D.H., A.K.L., M.C., N.A.S., D.J.D., C.K., J.J.J., J.H.S., M.Bau, V.B., J.C., K.D.H., C.M.L., B.D. and J.O. wrote and edited the manuscript with input from all authors. J.J.J., N.A.S., J.H.S., D.J.D., M.Bau, B.B. and J.C. prepared figures. T.D.H., B.D., M.C., J.O., T.J.B., K.D.H., D.J.D., V.B., C.K. and K.S. supervised the work. T.D.H and S.M. managed the project.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Timothy D. Harris.

Reviewer Information Nature thanks M. Maharbiz and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains the probe technical description and design phases 1–3.

  2. 2.

    Life Sciences Reporting Summary