NIC Wiki

Imaging of thick (>50 um) tissue sections is often improved by clearing of the samples - treating them so that the normally opaque sample becomes clear. In 2007, we tested a number of clearing methods in conjunction with Nan Tang. The results are summarized in this white paper. Since then, other clearing methods have been published:

• Passive Clarity (PACT) clearing has been used successfully by a number of UCSF labs.
• The Scale protocol has been published by the Miyawaki lab, which uses 4M urea to render whole mouse embryos essentially transparent.
• A recent paper shows that dehydration with tetrahydrofuran and clearing with dibenzyl ether preserves GFP fluorescence better than ethanol dehydration and clearing with BABB.
• CLARITY uses electrophoresis with SDS to clear very thick brain tissue.
• SeeDB uses fructose and thioglycerol to clear tissue and appears to work about as well as Scale.
• Here is a detailed protocol for fixing and mounting dragonfly tissue in 2,2-TDE.
• 3DISCO uses tissue dehydration in THF and clearing with dibenzyl ether. It clears quickly and is at least somewhat compatible with GFP.
• Citifluor mounting media are supposed to clear well (Confocal Listserv post from Sean Speese, 10/22/2013).
• A recent review compares a variety of these clearing methods.