The problem: When staining tissues, it is difficult to see through tissue and so most of the time what is done is to section the tissue and then stain for specific proteins to see their distribution within the tissue. Sectioning also enables the tissue to become accessible for the reagents that are used to stain the tissue.
However, for brain as a tissue, it will be great to see the connections between within the neurons and see the whole brain.
Solution: Treat the tissue to make it transparent. Karl Diesseroth from Stanford have enabled the brain tissue to become transparent and enables antibodies to stain the entire brain. The cool factor is the ability to see the distribution of any specific protein all over the brain in glorious three dimensions. They have created an hydrogel that replaces the lipid in the brain and then removed the lipid with electrophoresis. Once that is done then the entire organ like the brain can be stained and looked at whole.
The images look fantastic. Look at the link below for more details but the video from NATURE is very impressive.
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