Will you be able to share the protocol you followed for CLARITY tissue clearing? I would like to try this technique.

That's very interesting indeed, although 5 weeks is rather long...! It looks quite transpartent indeed, have you been able to image endogenous fluorophores and/or perform immunostaining, and to compare to ETC?

@Mayur Parmar, the protocol is the same as the Deisseroth paper, with the only change being to leave the brain in the second 37 degree wash in clearing solution until you see clearing. We are running a trial now to see if changing the clearing solution more often leads to a quicker clearing.

@Julien Bouvier, this particular sample was never intended to be imaged because it only has endogenous fluorescence in the opposite hemisphere (it was plasmid transfected via in utero electroporation). The only reason we kept the sample was that it was accidentally left in the incubator and when I went to check on other samples I noticed it had cleared significantly. So we are attempting a full brain ihc staining for calretinin with this sample and hopefully try some imaging when it is done (6 weeks later) :(

Please keep us updated, Gregory! We're trying the passive approach here, and I'm sure the researcher in charge of the project would love to know if the tubes need as much baby-sitting as they're giving them. 

I have done passive clearing on rodent brain slices, 2-3mm thick. Works like a charm. Electeophoresis induced too much damage, I found. I tried electrophoresis on a half hemisphere, and it just looked like a yellow loogie in the end, despite temperature and voltage being low (~35C and 20V respectively). I also did passive clearing on a larger chunk (about 2cm^3), and a half hemisphere, but at a 4% bis-acrylamide concentration it took almost 4 months. However, it was not at 37C most of the time, and I somewhat neglected it. No damage, looks great, just slow. The slices took about 3 weeks at 37C if it was below 3% (closer to 4-5 weeks for 3-4%), and it worked beautifully (Without changing the clearing solution at all). I do antibody staining for about 4 days on the slices.

I tried a 0.5% concentration on entire half hemispheres passively, but its not really clearing, just slowly disintegrating..

So far the passive approach on thick slices is a clear winner for me. 

The Clarity Wiki implies that omission of bis-acrylamide (using only acrylamide) in the hydrogel polymerization process allows the tissue to be more porous. Perhaps that hastens clearing time?

http://wiki.claritytechniques.org/index.php/Solutions#Changes_to_the_hydrogel_solution_composition

http://wiki.claritytechniques.org/index.php/Passive_Clearing#Strategies_to_increase_clearing_speed

Yang et al. (Cell, 2014) did this acrylamide-only hydrogel prep for tissue that had been pre-fixed, and their brains were cleared in substantially less time, on the order of days instead of weeks. They did use a little more SDS in their clearing solution, however (8% instead of the original protocol's 4%).

Link to extended PDF: http://www.cell.com/cell/pdfExtended/S0092-8674(14)00931-3

Additionally, Poguzhelskaya et al. (Molecular Neurodegeneration, 2014) did this in 1-1.5 mm thick coronal mouse brain sections as Annabelle had mentioned, having first perfused mice with the hydrogel solution. Their clearance time was 7-10 days.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4049387/

I'm also just starting this passive clearing approach, so I'm only beginning to try these approaches. Best of luck to those also starting up this useful technique in their labs.