Wide-area all-optical neurophysiology in acute brain slices

Samouil L. Farhi, Vicente J. Parot, Abhinav Grama, Masahito Yamagata, Ahmed S. Abdelfattah, Yoav Adam, Shan Lou, Jeong Jun Kim, Robert E. Campbell, David D. Cox, Adam E. Cohen*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


Optical tools for simultaneous perturbation and measurement of neural activity open the possibility of mapping neural function over wide areas of brain tissue. However, spectral overlap of actuators and reporters presents a challenge for their simultaneous use, and optical scattering and out-of-focus fluorescence in tissue degrade resolution. To minimize optical crosstalk, we combined an optimized variant (eTsChR) of the most blue-shifted channelrhodopsin reported to-date with a nuclear-localized red-shifted Ca2+ indicator, H2B-jRGECO1a. To perform wide-area optically sectioned imaging in tissue, we designed a structured illumination technique that uses Hadamard matrices to encode spatial information. By combining these molecular and optical approaches we made wide-area functional maps in acute brain slices from mice of both sexes. The maps spanned cortex and striatum and probed the effects of antiepileptic drugs on neural excitability and the effects of AMPA and NMDA receptor blockers on functional connectivity. Together, these tools provide a powerful capability for wide-area mapping of neuronal excitability and functional connectivity in acute brain slices.

Original languageAmerican English
Pages (from-to)4889-4908
Number of pages20
JournalJournal of Neuroscience
Issue number25
StatePublished - 19 Jun 2019
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by the Howard Hughes Medical Institute, by an NSF Graduate Research Fellowship to S.L.F, by a Becas Chile scholarship to V.J.P., and work in David Cox’s laboratory was supported by IARPA (contract D16PC00002)andtheMindBrainBehaviorFacultyAwardofHarvard.ConstructswillbemadeavailableonAddgene. Code for Hadamard pattern generation and image reconstruction, as well as raw data examples are linked in Materials and Methods. We thank Vaibhav Joshi, Katherine Williams, and Melinda Lee for technical assistance, Bernardo Sabatini for Rbp4-Cre mice, Christopher Werley for assistance with the microscope design, Daryl Lim for providing HiLo reconstruction code, and Joshua Sanes for support for the cloning of H2B-jRGECO1a.

Publisher Copyright:
© 2019, Society for Neuroscience. All rights reserved.


  • Brain slice
  • Calcium imaging
  • Microscopy
  • Optogenetics


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