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CALM Microscopy Wiki
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  • 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 2013 review compares a variety of these clearing methods.

  • A 2021 review  covering current clearing methods and imaging cleared tissues