You might try autofluorescence compensation. Thjat technique has worked
well in our Facility on cultured cells with high autofluorescence. A
reference is enclosed.
-Marty Bigos
Stanford Shared FACS Facility
Alberti S; Bucci C; Fornaro M; Robotti A; Stella M.
Immunofluorescence analysis in flow cytometry: better selection of
antibody-labeled cells after fluorescence overcompensation in the red
channel.
Journal of Histochemistry and Cytochemistry, 1991 May, 39(5):701-6.