Neuropixels

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Neuropixels probes (or "Neuropixels") are electrodes developed in 2017 to record the activity of hundreds of neurons in the brain. The probes are based on CMOS technology; the original versions have 960 recording sites arranged in two rows on a thin, 1-cm long shank. [1] [2]

Contents

The probes are used in hundreds of neuroscience laboratories including the International Brain Laboratory, to record brain activity mostly in mice and rats. By revealing the activity of vast numbers of neurons, Neuropixels probes are allowing new approaches [3] to the study of brain processes such as sensory processing, decision making, [4] internal state, [5] and emotions [6] and to create brain-machine interfaces. [7] [8]

History

The probes were first announced in 2017. [9] They were developed by a consortium of IMEC, the Janelia Research Campus of HHMI, the Allen Institute for Brain Science, and University College London. Funding was provided by the Howard Hughes Medical Institute (HHMI), the Wellcome Trust, the Gatsby Charitable Foundation and the Allen Institute for Brain Science. They are fabricated by IMEC, an electronics research center in Belgium.

In 2021 a new and improved version, NeuroPixels 2.0, was announced. [10] [11] In 2025, a new version that also includes dual-color optogenetic simulation was introduced. [12]

Neuropixels was originally developed only for use in experimental animals, but by 2022, Neuropixels probes were inserted in human patients. [13]

Data

Each pixel of the NeuroPixels probe records the extra-cellular voltage present at that spot of the brain. In general this is composed of two components - the local field potential, which is a slowly varying signal that is a sum of activity in the region, and the action potentials, which are short, fast transients, largely from neurons that are very close to the electrode. Neuropixels breaks these into two bands for processing, as the 10-bit resolution of the A/D converters cannot cover both cases simultaneously. The LFP band is 0.5-1000 Hz and sampled at 2.5 KHz, and the AP band is 0.3-10 KHz and sampled at 30 KHz. [9]

Data processing

Each individual pixel receives contributions from many neurons, and conversely a single neuron can contribute to many pixels. Untangling these contributions, to compute the activity of particular neurons, requires a process known as spike sorting. This is computationally expensive, and needed new development to be practical with the large number of channels enabled by NeuroPixels. [14] [15] This development is on-going as new versions of Neuropixels continue to increase the amount of data that can be collected. [16]

Uses

Among many other uses, researchers have used multiple Neuropixels probes in the same animal to conduct surveys of spiking activity from tens of thousands of neurons simultaneously, in six cortical and two thalamic regions of the brain. [17] The data from this survey is openly available.

References

  1. ↑ "How to make sense of the brain's billions of neurons | Wellcome". wellcome.ac.uk. 31 October 2018. Archived from the original on 2020-03-03. Retrieved 2020-08-25.
  2. ↑ "A new nerve-cell monitor will help those studying brains". The Economist. ISSN   0013-0613 . Retrieved 2022-11-01.
  3. ↑ Hernandez, Daniela (2018-06-15). "The Quest to Decode the Brain". Wall Street Journal. ISSN   0099-9660 . Retrieved 2020-08-25.
  4. ↑ Steinmetz, Nicholas A.; Zatka-Haas, Peter; Carandini, Matteo; Harris, Kenneth D. (December 2019). "Distributed coding of choice, action and engagement across the mouse brain". Nature. 576 (7786): 266–273. doi:10.1038/s41586-019-1787-x. ISSN   1476-4687. PMC   6913580 . PMID   31776518.
  5. ↑ Allen, William E.; Chen, Michael Z.; Pichamoorthy, Nandini; Tien, Rebecca H.; Pachitariu, Marius; Luo, Liqun; Deisseroth, Karl (2019-04-19). "Thirst regulates motivated behavior through modulation of brainwide neural population dynamics". Science. 364 (6437): 253. Bibcode:2019Sci...364..253A. doi:10.1126/science.aav3932. ISSN   0036-8075. PMC   6711472 . PMID   30948440.
  6. ↑ Abbott, Alison (2020-08-11). "Inside the mind of an animal". Nature. 584 (7820): 182–185. Bibcode:2020Natur.584..182A. doi: 10.1038/d41586-020-02337-x . PMID   32782378.
  7. ↑ "How brains and machines can be made to work together". The Economist. ISSN   0013-0613 . Retrieved 2020-08-25.
  8. ↑ Markoff, John (2019-07-16). "Elon Musk's Neuralink Wants 'Sewing Machine-Like' Robots to Wire Brains to the Internet". The New York Times. ISSN   0362-4331 . Retrieved 2020-08-25.
  9. 1 2 Jun, James J.; Steinmetz, Nicholas A.; Siegle, Joshua H.; Denman, Daniel J.; Bauza, Marius; Barbarits, Brian; Lee, Albert K.; Anastassiou, Costas A.; Andrei, Alexandru; Aydın, Çağatay; Barbic, Mladen (2017-11-08). "Fully Integrated Silicon Probes for High-Density Recording of Neural Activity". Nature. 551 (7679): 232–236. Bibcode:2017Natur.551..232J. doi:10.1038/nature24636. ISSN   0028-0836. PMC   5955206 . PMID   29120427.
  10. ↑ "Neuropixels 2.0 Probe".
  11. ↑ Steinmetz, Nicholas A.; Aydin, Cagatay; Lebedeva, Anna; Okun, Michael; Pachitariu, Marius; Bauza, Marius; Beau, Maxime; Bhagat, Jai; Böhm, Claudia; Broux, Martijn; et al. (2021). "Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings". Science. 372 (6539). American Association for the Advancement of Science: eabf4588. doi:10.1126/science.abf4588.{{cite journal}}: CS1 maint: article number as page number (link)
  12. ↑ Lakunina, Anna; Socha, Karolina Z; Ladd, Alexander; Bowen, Anna J; Chen, Susu; Colonell, Jennifer; Doshi, Anjal; Karsh, Bill; Krumin, Michael; Kulik, Pavel; et al. (2025). "Neuropixels Opto: Combining high-resolution electrophysiology and optogenetics". bioRxiv. Cold Spring Harbor Laboratory. doi:10.1101/2025.02.04.636286.
  13. ↑ Paulk, Angelique C.; Kfir, Yoav; Khanna, Arjun R.; Mustroph, Martina L.; Trautmann, Eric M.; Soper, Dan J.; Stavisky, Sergey D.; Welkenhuysen, Marleen; Dutta, Barundeb; Shenoy, Krishna V.; Hochberg, Leigh R.; Richardson, R. Mark; Williams, Ziv M.; Cash, Sydney S. (February 2022). "Large-scale neural recordings with single neuron resolution using Neuropixels probes in human cortex" . Nature Neuroscience. 25 (2): 252–263. doi:10.1038/s41593-021-00997-0. ISSN   1546-1726. PMID   35102333. S2CID   246442929.
  14. ↑ Pachitariu, Marius; Steinmetz, Nicholas; Kadir, Shabnam; Carandini, Matteo; Harris, Kenneth D. (2016). "Kilosort: realtime spike-sorting for extracellular electrophysiology with hundreds of channels" (PDF). BioRxiv. Cold Spring Harbor Laboratory: 061481.
  15. ↑ Pachitariu, Marius; Steinmetz, Nicholas A.; Kadir, Shabnam N.; Carandini, Matteo; Harris, Kenneth D. (2016). "Fast and accurate spike sorting of high-channel count probes with KiloSort" (PDF). Advances in neural information processing systems. Vol. 29.
  16. ↑ Buccino, Alessio P; Sridhar, Arjun; Feng, David; Svoboda, Karel; Siegle, Joshua H (2025). "Efficient and reproducible pipelines for spike sorting large-scale electrophysiology data". bioRxiv. Cold Spring Harbor Laboratory: 2025–11. doi:10.1101/2025.11.12.687966.
  17. ↑ Siegle, Joshua H; Jia, Xiaoxuan; Durand, Séverine; Gale, Sam; Bennett, Corbett; Graddis, Nile; Heller, Greggory; Ramirez, Tamina K; Choi, Hannah; Luviano, Jennifer A; et al. (2021). "Survey of spiking in the mouse visual system reveals functional hierarchy". Nature. 592 (7852). Nature Publishing Group UK London: 86–92. doi:10.1038/s41586-021-03619-1.
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