Dyes which, when illuminated by an excitation beam of a certain wavelength, are able to absorb the energy of this radiation and virtually immediately emit radiation of a longer wavelength (fluoresce).
Fluorophores are most often small molecules of organic compounds with aromatic nuclei, or even whole proteins - the best known is the so-called GFP (Green Fluorescent Protein). GFP is specific in that it fluoresces green when exposed to blue light.
Fluorophores have important applications in e.g. flow cytometry (flow sorting) for fast and efficient separation of cells and particles, specifically GFP serves as a reporter gene for visualization of protein expression, 3D tracking or colocalization of different proteins.