Adaptive optics for confocal microscopy in thick samples

Fluorescence imaging and clearing on mouse brains are two techniques widely used in neurosciences. Whole brain imaging at depth remains challenging though, even for cleared samples because of sample induced optical aberrations. The development of adaptive optics corrected fluorescent microscopes for thick samples will help image the neural network in whole rodent clarified brains. To optimize such a system, we need to characterize the optical aberrations induced by the cleared rodent brain. In our project, we combine a confocal microscope and two wavefront sensors (Shack-Hartmann and pyramid) to have independent sensing and probe the performance of each sensor. In this paper, we describe the experimental setup of the microscope and we present challenges induced by thick samples on aberration measurements in confocal microscopy.