Generally the best way is to use a fluorescent dye, assuming you have the
capability. BCECF (bis-Carboxyethylcarboxyfluorescein, if memory serves)
is probably one of the most widely used for this purpose. You can also
use any of a variety of other fluoresceins.
Yeast is trickier as they have a tendency to stuff the cell permeant forms
of these dyes into their vacuoles. I'm sure there are ways around this.
Try contacting one of the companies that specializes in Fluorescent