Spectral flow cytometry and conventional flow cytometry share similar designs in fluidics and lasers. The main differences between the two techniques are the optics and detectors.

• Optics: Conventional flow cytometry uses mirrors and optical filters to block, reflect, or transmit a photon based on its wavelength, while spectral flow cytometers employ employs light dispersion elements, such as prisms and spectrographs, to disperse photons according to wavelength.
• Detectors: The detectors used in conventional flow cytometry are usually individual photodiode (PD) or photomultiplier tube (PMT). However, to measure the continuous spectrum produced by the dispersive elements, a linear array of detectors is required. The common detectors used in spectral flow cytometry are arrays of charge coupled devices (CCDs) and multianode PMTs.