This recent paper describes an improved dehydration and clearing method for clearing mouse brains and preserving GFP fluorescence. The use tetrahydrofuran, instead of ethanol, for dehydration, and dibenzyl ether for clearing, and show superior results to the use of BABB or methyl salicylate. They claim this works better than the Miyawaki lab Scale protocol in adult mouse brain.
This is figure 3 from their paper – the left side is conventionally cleared; the right side with their new method:
Reference: Chemical Clearing and Dehydration of GFP Expressing Mouse Brains
Becker K, Jährling N, Saghafi S, Weiler R, Dodt H-U (2012) Chemical Clearing and Dehydration of GFP Expressing Mouse Brains. PLoS ONE 7(3): e33916. doi:10.1371/journal.pone.0033916