Flow Cytometry is a technique which can objectively examine, quantify and separate single cells on the basis of one or more parameters. Flow cytometry involves channeling individual cells in a narrow fluid stream past a laser beam, which is usually oriented at a right angle to the flow. Optical sensors detect signals generated as the cells pass through the laser beam. The cells scatter the laser light in proportion to their size and "complexity" (e.g. presence of granules in their cytoplasm). Thus, cells can be identified based on their light scatter characteristics, and a population chosen (gated) for further analysis.

Antibodies coupled to fluorochromes (different fluorochromes emit different wavelengths of light upon excitation by a laser) are used to label or "stain" the cells so that each cell can be identified and quantitated based upon its fluorescence signal. A computer collects the fluorescence signature of each cell and displays the pattern of fluorescence for the user to analyze. In other applications, where one might want to separate cells which have a certain staining pattern from all other cells, the flow cytometry machine can direct those desired cells into a tube provided by the user. This is called fluorescence activated cell sorting (FACS).