Long-Term Optical Access to an Estimated One Million Neurons in the Live Mouse Cortex

Cell Rep. 2016 Dec 20;17(12):3385-3394. doi: 10.1016/j.celrep.2016.12.004.


A major technological goal in neuroscience is to enable the interrogation of individual cells across the live brain. By creating a curved glass replacement to the dorsal cranium and surgical methods for its installation, we developed a chronic mouse preparation providing optical access to an estimated 800,000-1,100,000 individual neurons across the dorsal surface of neocortex. Post-surgical histological studies revealed comparable glial activation as in control mice. In behaving mice expressing a Ca2+ indicator in cortical pyramidal neurons, we performed Ca2+ imaging across neocortex using an epi-fluorescence macroscope and estimated that 25,000-50,000 individual neurons were accessible per mouse across multiple focal planes. Two-photon microscopy revealed dendritic morphologies throughout neocortex, allowed time-lapse imaging of individual cells, and yielded estimates of >1 million accessible neurons per mouse by serial tiling. This approach supports a variety of optical techniques and enables studies of cells across >30 neocortical areas in behaving mice.

Keywords: brain imaging; calcium imaging; dendrites; dendritic spines; fluorescence imaging; mouse behavior; neocortex; neural ensembles; two-photon microscopy.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Calcium / chemistry
  • Dendrites / ultrastructure*
  • Dendritic Spines / ultrastructure*
  • Mice
  • Microscopy, Fluorescence
  • Neocortex / ultrastructure*
  • Pyramidal Cells / ultrastructure*
  • Single-Cell Analysis
  • Time-Lapse Imaging


  • Calcium