A sample analyzing apparatus for performing an optical-based measurement on a sample includes a housing, a first light source, excitation optics, a first light detector, emission optics, and a monitoring system, all of which are disposed in the housing. The monitoring system is configured for monitoring a movable component disposed in the housing. The monitoring system includes one or more light sources for illuminating the movable component, and one or more light detectors for detecting light reflected from the movable component in response to being illuminated.