The cellular characteristics measured include the expression of cell surface and intracellular molecules, various cell types in heterogeneous cell populations, purity of isolated subpopulations, and single-cell size and volume. The resulting emitted photons are collected and become the data that identifies characteristics about the cells in question. It is a powerful technique commonly used in the life sciences.

This technique is also often used for high-throughput measurement of antigens on live cells. There is no better option in this case, as the technique utilizes fluorescent markers on antibodies or other proteins in order to quantifiably detect changes in protein expression via excitation of the various fluorescent markers. Antibodies allow scientists to detect a specific antigen, making them useful tools for protein characterization on the surface of live cells.

The antibodies can be directly labeled with a fluorescent marker—such as FITC (fluorescein isothiocyanate)—or can be visualized by binding to a secondary antibody that is labeled. This allows flow cytometry to analyze or sort cells based on more than one color, each representing a different antigen that is bound by a different antibody.

Over the past 30 years, single-cell flow cytometry analysis has become an indispensable tool for many scientific researchers and clinicians working in the life sciences performing data analysis and, more specifically, cell analysis.

The evolving technology ensures its application in a number of fields, including cell biology, drug discovery, cancer research, neuroscience, stem cell research, pathology, immunology, hematology, plant biology, food science, and marine biology.