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clearing_methods [2013/10/23 11:07]
kthorn
clearing_methods [2016/01/11 09:50]
kthorn
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 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 {{:​mounting_media_tests.pdf|white paper}}. Since then, other clearing methods have been published: 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 {{:​mounting_media_tests.pdf|white paper}}. Since then, other clearing methods have been published:
  
 +  * [[http://​www.sciencedirect.com/​science/​article/​pii/​S0092867414009313|Passive Clarity (PACT)]] clearing has been used successfully by a number of UCSF labs.
   * The [[http://​www.ncbi.nlm.nih.gov/​pubmed/​21878933|Scale protocol]] has been published by the Miyawaki lab, which uses 4M urea to render whole mouse embryos essentially transparent.   * The [[http://​www.ncbi.nlm.nih.gov/​pubmed/​21878933|Scale protocol]] has been published by the Miyawaki lab, which uses 4M urea to render whole mouse embryos essentially transparent.
   * A [[http://​www.plosone.org/​article/​info%3Adoi%2F10.1371%2Fjournal.pone.0033916|recent paper]] shows that dehydration with tetrahydrofuran and clearing with dibenzyl ether preserves GFP fluorescence better than ethanol dehydration and clearing with BABB.   * A [[http://​www.plosone.org/​article/​info%3Adoi%2F10.1371%2Fjournal.pone.0033916|recent paper]] shows that dehydration with tetrahydrofuran and clearing with dibenzyl ether preserves GFP fluorescence better than ethanol dehydration and clearing with BABB.
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   * [[http://​www.nature.com/​neuro/​journal/​v16/​n8/​full/​nn.3447.html|SeeDB]] uses fructose and thioglycerol to clear tissue and appears to work about as well as Scale.   * [[http://​www.nature.com/​neuro/​journal/​v16/​n8/​full/​nn.3447.html|SeeDB]] uses fructose and thioglycerol to clear tissue and appears to work about as well as Scale.
   * Here is a [[http://​cshprotocols.cshlp.org/​content/​2012/​9/​pdb.prot069625.full|detailed protocol]] for fixing and mounting dragonfly tissue in 2,2-TDE.   * Here is a [[http://​cshprotocols.cshlp.org/​content/​2012/​9/​pdb.prot069625.full|detailed protocol]] for fixing and mounting dragonfly tissue in 2,2-TDE.
 +  * [[http://​www.nature.com/​nprot/​journal/​v7/​n11/​full/​nprot.2012.119.html|3DISCO]] uses tissue dehydration in THF and clearing with dibenzyl ether. It clears quickly and is at least somewhat compatible with GFP.
   * [[http://​www.citifluor.com/​non_hardening_antifadents.php|Citifluor]] mounting media are supposed to clear well (Confocal Listserv post from Sean Speese, 10/​22/​2013).   * [[http://​www.citifluor.com/​non_hardening_antifadents.php|Citifluor]] mounting media are supposed to clear well (Confocal Listserv post from Sean Speese, 10/​22/​2013).
   * A [[http://​onlinelibrary.wiley.com/​doi/​10.1002/​anie.201306039/​full|recent review]] compares a variety of these clearing methods.   * A [[http://​onlinelibrary.wiley.com/​doi/​10.1002/​anie.201306039/​full|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