Technical Report

Precise multimodal optical control of neural ensemble activity

  • Nature Neurosciencevolume 21pages881893 (2018)
  • doi:10.1038/s41593-018-0139-8
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Understanding brain function requires technologies that can control the activity of large populations of neurons with high fidelity in space and time. We developed a multiphoton holographic approach to activate or suppress the activity of ensembles of cortical neurons with cellular resolution and sub-millisecond precision. Since existing opsins were inadequate, we engineered new soma-targeted (ST) optogenetic tools, ST-ChroME and IRES-ST-eGtACR1, optimized for multiphoton activation and suppression. Employing a three-dimensional all-optical read–write interface, we demonstrate the ability to simultaneously photostimulate up to 50 neurons distributed in three dimensions in a 550 × 550 × 100-µm3 volume of brain tissue. This approach allows the synthesis and editing of complex neural activity patterns needed to gain insight into the principles of neural codes.

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We thank M. Feller, A. Naka, and J. Brown for critical feedback on the manuscript and discussions. We thank C. Baker and M. Bolton for soma-targeted ChR2 AAVs. We thank M. Li and the UC Berkeley Vision Science Core, Gene Delivery Module, for preparation of AAVs (supported by NIH Core Grant P30 EY003176). We deeply appreciate the efforts of D. Chu, C. Douglas, and R. Hakim for important technical assistance. We thank D. Taylor for help with mouse work and histology. H.A. is a New York Stem Cell Foundation-Robertson Investigator. This work was supported by The New York Stem Cell Foundation and by grants from the Arnold and Mabel Beckman Foundation, NINDS grant DP2NS087725-01, the McKnight Foundation, NINDS award F32NS095690-01 to A.R.M., the Simon’s Foundation Collaboration for the Global Brain award 415569 to I.A.O., and a fellowship from the David and Lucille Packard Foundation to L.W. This research was developed with funding from the Defense Advanced Research Projects Agency (DARPA), Contract No. N660011-17-C-4015.

Author information

Author notes

  1. These authors contributed equally: Alan R. Mardinly, Ian Antón Oldenburg, Nicolas C. Pégard.


  1. Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA

    • Alan R. Mardinly
    • , Ian Antón Oldenburg
    • , Nicolas C. Pégard
    • , Savitha Sridharan
    • , Kirill Chesnov
    • , Stephen G. Brohawn
    •  & Hillel Adesnik
  2. Department of Electrical Engineering & Computer Sciences, University of California, Berkeley, Berkeley, CA, USA

    • Nicolas C. Pégard
    •  & Laura Waller
  3. Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA, USA

    • Evan H. Lyall
  4. Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA

    • Stephen G. Brohawn
    •  & Hillel Adesnik


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A.R.M., I.A.O., N.C.P. and H.A conceived the project and built the system. A.R.M. designed and performed all experiments involving excitatory opsins. I.A.O. designed and performed all experiments involving inhibitory opsins. N.C.P. designed and assembled the light paths and wrote custom holography software. S.S. performed cloning, mutagenesis, cell culture, and one-photon recordings in CHO cells. A.R.M., I.A.O., N.C.P., and E.H.L. wrote code and developed software for experimental control. K.C. performed histology. S.G.B. performed modeling of the Chronos pore region. L.W. contributed expertise on holographic design. A.R,M., I.A.O., N.C.P., and H.A. wrote the manuscript.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Hillel Adesnik.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Figures 1–23

  2. Reporting Summary

  3. Supplementary Table 1 – Optical Setup References

    This table provides details on each optical stimulation path used in this study and provides a quick reference to determine which experiments were performed using each setup

  4. Supplementary Table 2 – 3D-SHOT 2.0

    This table provides technical details and a calculation tool to allow readers to set up a 3D-SHOT stimulation path

  5. Supplementary Video 1 – SLM performance limitations for high speed 3D-SHOT

    This video demonstrates high speed switching of holograms at 300 Hz

  6. Supplementary Video 2 – All-Optical Ensemble Stimulation in 3D

    Average dF/F movies of ensembles stimulation data at 30 Hz as in Fig7-8