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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 white paper. Since then, other clearing methods have been published:
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.
mounting media are supposed to clear well (Confocal Listserv post from Sean Speese, 10/22/2013).