How does fluorescence work in flow cytometry?

When a fluorophore is coupled to the cells of interest, it absorbs the light from the laser. this light is emitted through emission of photons at a higher wavelength than the incoming wavelength (this is because some energy is lost to heat and vibration). the detector is placed in such a way that it detects the emission wavelength at its emission peak. the most widely used fluorophores for labelling antibodies are FITC, phycoerythrin (PE) and allophycocyanin (APC). when mutliple fluorophores are used, there will be some spectral overlap (overlap between the emission spectra). this can be corrected for by substrating a fraction of one fluorophore from another, called compensation.