Since biological samples generally do not have good contrast, fluorescence observation is　incorporated in the process to improve contrast.

Many laser scanning microscopes utilize the confocal optical system where a pinhole is placed at the focal point in order to condense light emitted from a sample in front of the detector. As the confocal optical system only detects fluorescence that is present at a location extremely close to the sample’s focal point, the optical resolution in the sample’s depth direction in particular is far superior to that of wide-field microscopes.

However, when the pinhole blocks light emitted from outside the focal point, less signal light reaches the detector. For this reason, high-sensitive detectors, such as photomultiplier tubes (PMT), hybrid photo detectors (HPD), and MPPCs (SiPM), are commonly used with the system.