Marketed by a number of distributors, the cyanine dyes (Cy2, Cy3, Cy5, Cy7, and their derivatives) are readily available as reactive dyes or fluorophores coupled to a wide variety of secondary antibodies, dextrin, streptavidin, and egg-white avidin. The cyanine dyes generally have broader absorption spectral regions than members of the Alexa Fluor family, making them somewhat more versatile in the choice of laser excitation sources for confocal and fluorescence microscopy. For example, using the 547-nanometer spectral line from an argon-ion laser, Cy2 is about twice as efficient in fluorescence emission as Alexa Fluor 488. In an analogous manner, the 514-nanometer argon-ion laser line excites Cy3 with a much higher efficiency than Alexa Fluor 546, a spectrally similar probe. Emission profiles of the cyanine dyes are comparable in spectral width to the Alexa Fluor series.

The PtK2 cell culture appearing in the digital image above was immunofluorescently labeled with primary anti-tubulin mouse monoclonal antibodies followed by goat anti-mouse Fab fragments conjugated to Cy3. The epithelial cells were also stained with DAPI, which preferentially binds to nuclear DNA. Images were recorded in grayscale with a QImaging Retiga Fast-EXi camera system coupled to an Olympus BX-51 microscope equipped with bandpass emission fluorescence filter optical blocks provided by Omega Optical. During the processing stage, individual image channels were pseudocolored with RGB values corresponding to each of the fluorophore emission spectral profiles.