The selection of fluorophores depends on:

1. Instrument set-up. For example, availability of light sources, filter sets, and detection systems.
   
   
2. Degree of colour separation desired for multiple labeling. For example, Rhodamine Red-X (RRX) and Texas Red (TR) give better separation from fluorescein than tetramethyl rhodamine (TRITC).
   
   
3. Sensitivity required. For example, Cy3 and Cy5 are brighter than other fluorophores.