Anatomical studies of complete brains are complicated by the fact that visible light does not penetrate deep into the brain. There are several solutions to this problem, the most important ones are to either make the tissue transparent ("tissue clearing
", used for samples for our Santoku microscope
) or to physically section the brain into thin slices. Physically sectioning tissue can generate very high quality data, but it is complicated to re-combine the images from the individual sections in order to create a seamless representation of the complete brain.
Here we developed a microscope that overcomes this problem by sectioning the tissue after
the imaging - very similar to the way data are acquired with electron microscopes in the department of Moritz Helmstädter
. In our case we are using a standard vibratome and compine it with a 2p fluorescence laser scanning microscope. By using a 2p microscope we can combine optical and physical sectioning. By combining the strength of both approaches we can optimize image quality and acquisition time. A whole brain can be imaged in about 12 hours.
The optical design of the microscope was developed in our facility. The BakingTray software
, which controls all components, including the synchronization between microscope and vibratome, was developed by Rob Campbell
(Sainsbury Wellcome Center). We are grateful for providing this excellent tool.