Quantitative fluorescence microscopy is becoming an increasingly impor
tant tool in the study of cell biology. Fluorescence microscopy has lo
ng been used for qualitative characterizations of subcellular distribu
tions of proteins, lipids, nucleic acids, and ions, but quantifying th
ese distributions is complicated by a variety of optical, biological,
and physical factors. Many factors that complicate quantification of f
luorescence in cells can be circumvented by analyzing fluorescence rat
ios derived from pairs of fluorescence images. In this review we will
discuss the factors that affect fluorescence quantification, the advan
tages of quantifying fluorescence as a ratio, and give examples of how
fluorescence ratio microscopy is being applied in studies of cell bio
logy.