Researchers often use “flow cytometry” to refer to a method of analyzing cells on an aptly named flow cytometer.1 However, the term also encompasses techniques that enable researchers to characterize individual components on or within a specimen, most often cells, in an entire sample rapidly and in high dimension. 

In addition to cell analysis, cell sorting, sometimes referred to as fluorescence-activated cell sorting (FACS), is another common application of flow cytometry.2 While these two techniques and their instruments are similar, an important distinction lies in what happens to the sample after it is analyzed. 

The Specifics of Flow Cytometry

In flow cytometry, a pump draws the sample into the instrument and orients the individual cells into a single-file line for each one to pass in front of one or more lasers. Scientists instruct the computer to record information about various parameters on the cell including its size and rough composition. Detectors record information about the intensity and scattering pattern of the light after it leaves the cell. After laser interrogation, flow cell analyzers deposit all of the sample into a waste receptacle in the instrument. 

FACS: To Sort, or Not to Sort

Cell sorters operate almost identically to flow cytometers up until the cell leaves the laser. After this point, cell sorters break the stream of cells into droplets by oscillating.3 The computer rapidly calculates specified qualities of the cell, and based on those parameters, applies a charge to the individual droplet holding the cell. As the now-charged droplet continues to descend away from the laser, it passes through magnetic plates that attract or repel it toward collection tubes. Sorters today can separate cells into up to six different populations. 

  1. McKinnon KM. Curr Protoc Immunol. 2018;120(1):5.1.1-5.1.11
  2. Bonner WA, et al. Rev Sci Instrum. 1972;43(3):404-409
  3. Steinkamp JA, et al. Rev Sci Instrum. 1973;44(9):1301-1310