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Clearing Methods

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.
/var/www/html/dokuwiki/data/pages/clearing_methods.txt · Last modified: 2016/01/11 09:50 by kthorn