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Dear Pedro--

On 7/26/2011 9:26 AM, Pedro Almada wrote:

> If you are curious what it's for, it's for some of our users who image whole
> drosophila brains for structural information. Their common complaint is that
> half-way through their z-stack they loose image brightness until the last
> slices are barely visible. Clearing methods like Methyl salicilate aren't
> really adequate for neuronal structure I'm told, which leads me to consider
> this method.

This is a long shot, but is there any chance that they're over-staining 
their tissue?  If they're using high concentrations of their 
fluorophores, they may be absorbing most of the light in the top half of 
the tissue, leaving no photons for the bottom half.  Cutting back the 
concentration of secondary antibodies would be expected to improve 
penetration, if this were the case.

Good luck!

Martin Wessendorf

-- 
Martin Wessendorf, Ph.D.                   office: (612) 626-0145
Assoc Prof, Dept Neuroscience                 lab: (612) 624-2991
University of Minnesota             Preferred FAX: (612) 624-8118
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