Fluorescence imaging can be used for visualizing cellular components or metabolic products. To allow the detection of those, fluorescent dyes are used to stain certain cell structures, or they are used as markers for reaction products.

Epifluorescence microscopy is commonly used in life sciences employing an inverted microscope. The excitation light irradiates the sample through the objective lens. The emitted fluorescence passes the same objective before reaching the detector. In this setup, only reflected excitatory light can reach the detector, greatly enhancing the signal-to-noise ratio. A dichroic mirror reflects the emitted fluorescence towards the detector. The excitatory light is transmitted. The inverted microscope takes up space only below the specimen which allows the integration of a scanning head from the top to perform scanning probe experiments.