3D Optical microscopy for “ex-vivo” whole brain imaging

Abstract

The work presented in this paper focuses in understanding a light sheet microscope. Light sheet microscopy consists in a thin sheet of light which illuminates the observed sample in the plane orthogonal to the objective, thus allowing the observation of the internal structure. In this work we particularly focus in the impact of one of the main elements of such microscope: the slit. Optimizing different optical elements of a light sheet microscope to obtain images of cleared samples of animal brains about 2cm of diameter. This will allow obtaining microscopic images of organs in the centimetre range. In the optimization of a light sheet microscope several parameters are critical, like the slit aperture, the laser waist and the focal distance to the tube lens. Future developments of this setup will allow obtaining 3D reconstruction of interior structures, avoiding histological slicing of the specimens. The applications of this kind of microscopy in life sciences are numerous.