DAPI, Hoechst 33342 are excellent for this purpose assuming you have 
the appropriate filter sets on your scope for that wavelength. 
Alternatively if you are doing confocal with a far red laser you can 
use Draq-5 or Topro-3.


>Hello,
>
>    I am processing mouse brain sections for double-immunofluorescence and
>need to find a suitable counterstain.  I do not necessarily need the
>counterstain to be fluorescent, since the purpose of the counterstain
>is only to map the area of interest, but I want to make sure that
>whatever counterstain I use is not going to quench my fluoresence. I am
>using secondary-conjugated Alexa 488 and Streptavidin-Alexa 546.  I
>appreciate any and all advice.  Thanks in advance for your help!
>
>Best,
>Anna Beaudin
>Division of Nutritional Sciences
>Cornell University

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