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My basic experience is that optical clearing mostly acts by refractive index 
matching, but there is some evidence that agents like glycerol also disrupt 
collagen fibril structure that helps to reduce diffraction and I would imagine 
autofluorescence (Bui et al. Lasers in Surgery and Medicine 41:142–148 
(2009)).
I have been trying a wide variety of clearing agents for skeletal muscle. From 
my experience with clearing agents, 2,2 - Thiodiethanol 97% works very well to 
clear and match refractive index for immersion lenses, and allows imaging up to 
~200 microns using traditional confocal techniques. Potentially using 
multiphoton methods would get you substantially deeper, if that is available. 
However, even with multiphoton you have to consider the scattering coming 
back up through the tissue, which similarly reduces the optical resolution. 
Because of the nature of my experiments, intact scale is important and I have 
been hesitant to use ScaleA2 clearing during to the significant swelling 
exhibited by the tissues despite the ability to resolve deep into the tissue 
(~22% increase in volume). As an alternative to ScaleA2, it may be useful to 
try FocusClear (available from CedarLane Labs), which from my experiences 
makes tissues incredibly transparent (more so than TDE, and much more so 
than glycerol clearing, but it does not have the ideal 1.515/8 RI of oil). Using 
FocusClear has allowed me to see much deeper in the tissue (>500 microns, 
versus ~80 microns in 50/50 glycerol:pbs clearing). One issue to consider 
though is that it seems that far red fluorophore signal (DRAQ5, nuclear stain in 
my protocols) appears to be somewhat quenched with MountClear and TDE (so 
some increased background fluorescence)