Optical sectioning of biological tissues has become the method of choice for three-dimensional histological analyses.
This is particularly important in the brain were neurons can extend processes over large distances and often whole brain
tracing of neuronal processes is desirable. To allow deeper optical penetration, which in fixed tissue is limited by
scattering and refractive index mismatching, tissue-clearing procedures such as CLARITY have been developed.
CLARITY processed brains have a nearly uniform refractive index and three-dimensional reconstructions at cellular
resolution have been published. However, when imaging in deep layers at submicron resolution some limitations caused
by residual refractive index mismatching become apparent, as the resulting wavefront aberrations distort the microscopic
image. The wavefront can be corrected with adaptive optics. Here, we investigate the wavefront aberrations at different
depths in CLARITY processed mouse brains and demonstrate the potential of adaptive optics to enable higher resolution
and a better signal-to-noise ratio. Our adaptive optics system achieves high-speed measurement and correction of the
wavefront with an open-loop control using a wave front sensor and a deformable mirror. Using adaptive optics enhanced
microscopy, we demonstrate improved image quality wavefront, point spread function, and signal to noise in the cortex
of YFP-H mice.