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Fluorescence activated cell sorting (FACS) technology (Becton Dickinson) is based on flow cytometer technology, but in addition to simple cell characterization, FACS enables cells to be sorted into different containers. The principle is similar: cells labeled with fluorescent dyes or antibodies flow through a thin capillary and pass a light source, usually one or more laser beams. The emitted light is detected and characterizes the cell. At the end of the capillary, each cell is distributed into a single, small droplet that is charged electrically, trapped in an electric field with the opposite charge and led to its final container according to its fluorescence properties.

FACS can be used in several applications similar to those of flow cytometry. The additional cell sorting capabilities enable the separation of even viable cells, which is critical in clone selection, sperm sorting and other applications.