A method of detecting and quantifying viable cells in a sample. The method includes fluorescently staining the cells by adding a fluorescent dye into the sample or putting the sample in contact with the fluorescent dye. A quenching dye is then added to the stained sample, or the sample is put into contact with the quenching dye, at a pH different from the pH in the viable cells. The quenching dye used is permeable through the membrane of a viable cell and does not readily absorb fluorescence of the fluorescent dye at the pH in the viable cells, but absorbs the fluorescence of the fluorescent dye at the pH of the fluorescent dye. Next, the sample, now stained with the fluorescent dye and the quenching dye, is illuminated by an excitation light for the fluorescent dye at a pH different from the pH in the viable cells and the fluorescence emitted from the sample is collected and detected.