In confocal microscopy an object is scanned using a laser beam to build up the image a line at a time.
The microscope works in two basic modes - epifluorescence and reflection.
In epifluorescent mode, the laser excites fluorescence within the sample - this is either natural fluorescence (autofluorescence) or a fluorescent dye that has been attached to a specific site on the sample using an antibody label.
We can also use non-specific fluorescent dyes. Using different dye and laser combinations, we can simultaneously label different parts of the sample to differentiate specific features in 3D.