Note that laser beam can hit the traveling cells at straight or at a inclined angle. As described above, the angle at which the laser hits the cells will cause their properties to change depending on the cell cytoplasmic, nuclear and internal components. Through computational calculations, cells are separated into groups as shown in this diagram. The groups will be located in the histogram according to their properties, which can be enhanced by specific markers of which fluorochromes are the most useful at this point.
Cells have receptors sticking out of their membranes.
Antibodies can be made to recognize the entire or parts of these receptors and used later to separate cells bearing those molecules from those that do not have the same markers. The antibody-antigen complex is held in place by specific bonds and the marker can then be excited by the laser light that would excite a particular fluorochrome and not another. Monoclonal and polyclonal antibodies have already been made to most of the specific receptors that characterize cell populations in the blood and tissues. The antibodies are commercially available or can be obtained from investigators who develop the markers for their own research. Labeling cells inside pass the cell membrane is a whole different story that deserves a separate discussion.