Fluorescence microscopes take advantage of the difference in emission and transmission wavelengths of fluorophores to produce high contrast images. There are several fluorescent dyes that can freely diffuse into a living cell. Other fluorophores include fluorescent protein tags such as green fluorescent protein (GFP) or SNAP tags that can be expressed transgenically and fluorescently labeled antibodies that bind to molecules of interest in the cell. Therefore, fluorescent microscopy can be used to visualize microscopic processes that are impossible to visualize with other microscopy techniques.
Watch this short clip of cellular processes visualized with a fluorescent microscope.