Nicole,

Some authors have had some success using Sudan Black B to "quench"
autofluorescence. The Journal of Histochemistry and cytochemistry has
some articles on this if you do a PubMed search, you can find the
references (sorry, I'm having a busy day, so I can't provide them at the
moment).

Our imaging department also offers the availability of using spectral
imaging techniques. If you're fortunate enough to have good (read:
expensive) equipment, you can possibly use imaging to subtract the
autofluorescence.  Most of those types of techniques require microscopes
hooked up to computers to provide these techniques.

You may also have some luck switching to a different fluorophore that
won't show autofluorescence in the tissues as easily as the FITC or
green channels do.

Good luck!

Teri Johnson
Managing Director Histology Facility
Stowers Institute for Medical Research
1000 E. 50th St.
Kansas City, MO 64133

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