Disclosed is a system and method for characterizing optical filters in a flow cytometer and optionally checking the operation of detectors in the flow cytometer. In some embodiments, the system may utilize an LED board having an opening through which the fluorescence and side scatter beams, rays, or images pass and light emitting diodes around the opening that emit light having different spectral profiles. The different spectral profiles allow the system to identify the optical filters that are placed in the flow cytometer, to verify detector operation, to assist in instrumentation troubleshooting, and to provide a quantitative reference for detector comparison.