The Flow Cytometry

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A cell sample goes through a nozzle and is separated into a cell and a flow sheath in a tube on the other side. A laser hits this tube at a 90 degree angle and breaks off in two directions, one goes straight through and is labeled obscuration bar, the other at a 45 degree angle. There are 3 dichroic mirrors which break off and 3 filters. All 5 of the paths converge and are sent to an analysis workstation.
In flow cytometry, a mixture of fluorescently labeled and unlabeled cells passes through a narrow capillary. A laser excites the fluorogen, and the fluorescence intensity of each cell is measured by a detector. (credit: modification of work by “Kierano”/Wikimedia Commons)

OpenStax Microbiology

Fluorescently labeled antibodies can be used to quantify cells of a specific type in a complex mixture using flow cytometry, an automated, cell-counting system that detects fluorescing cells as they pass through a narrow tube one cell at a time. For example, in HIV infections, it is important to know the level of CD4 T cells in the patient’s blood; if the numbers fall below 500 per μL of blood, the patient becomes more likely to acquire opportunistic infections; below 200 per μL, the patient can no longer mount a useful adaptive immune response at all. The analysis begins by incubating a mixed-cell population (e.g., white blood cells from a donor) with a fluorescently labeled mAb specific for a subpopulation of cells (e.g., anti-CD4). Some experiments look at two cell markers simultaneously by adding a different fluorogen to the appropriate mAb. The cells are then introduced to the flow cytometer through a narrow capillary that forces the cells to pass in single file. A laser is used to activate the fluorogen. The fluorescent light radiates out in all directions, so the fluorescence detector can be positioned at an angle from the incident laser light.

The image above shows the obscuration bar in front of the forward-scatter detector that prevents laser light from hitting the detector. As a cell passes through the laser bar, the forward-scatter detector detects light scattered around the obscuration bar. The scattered light is transformed into a voltage pulse, and the cytometer counts a cell. The fluorescence from a labeled cell is detected by the side-scatter detectors. The light passes through various dichroic mirrors such that the light emitted from the fluorophore is received by the correct detector.

Data are collected from both the forward- and side-scatter detectors. One way these data can be presented is in the form of a histogram. The forward scatter is placed on the y-axis (to represent the number of cells), and the side scatter is placed on the x-axis (to represent the fluoresence of each cell). The scaling for the x-axis is logarithmic, so fluorescence intensity increases by a factor of 10 with each unit increase along the axis. The graph below depicts an example in which a culture of cells is combined with an antibody attached to a fluorophore to detect CD8 cells and then analyzed by flow cytometry. The histogram has two peaks. The peak on the left has lower fluorescence readings, representing the subset of the cell population (approximately 30 cells) that does not fluoresce; hence, they are not bound by antibody and therefore do not express CD8. The peak on the right has higher fluorescence readings, representing the subset of the cell population (approximately 100 cells) that show fluorescence; hence, they are bound by the antibody and therefore do express CD8.

A graph with fluorescence on the X axis and Cell count on the Y axis. The first peak reaches approximately 30 and is labeled do not express CD8. The second peak reaches about 100 and is labeld do express CD8.
Flow cytometry data are often compiled as a histogram. In the histogram, the area under each peak is proportional to the number of cells in each population. The x-axis is the relative fluorescence expressed by the cells (on a log scale), and the y-axis represents the number of cells at a particular level of fluorescence.

Source: OpenStax Microbiology


Parker, N., Schneegurt, M., Thi Tu, A.-H., Forster, B. M., & Lister, P. (n.d.). Microbiology. Houston, Texas: OpenStax. Access for free at: