Shameless plug: 3Scan [1], a company spun off from a university in Arizona (if I'm not mistaken) and partially funded by Peter Thiel's Breakout Labs grant is making a robot that is capable of doing this entire procedure with absolutely minimal human involvement.
They can already do a full 3d map of blood vessels and neurons (with stains) in a mouse brain within a few days and store it on a TB hard drive (I'm told an equivalent for the human brain would be a petabyte but their slices might be thinner). This is a procedure that would take months if not years to do by hand (they do a full analysis on all of the slices to reproduce a 3d model afterwards).
This paper was done mostly by hand but soon we'll be able to do it quickly and automatically.
[1] http://www.3scan.com/