Scientists have come up with a way to make whole brains transparent, so they can be labelled with molecular markers and imaged using a light microscope. The technique, called CLARITY, enabled its creators to produce the detailed 3D visualisations you see in this video. It works in mouse brains and human brains; here the team use it to look into the brain of a 7-year-old boy who had autism.
Original research paper: http://dx.doi.org/10.1038/nature12107
Nature News story: http://www.nature.com/news/see-through-brains-clarify-connections-1.12768