An embodiment of a microscope system is described that comprises a sample stage configured to position a sample; and a spectrometer comprising an interferometer configure to provide a light beam to the sample stage and one or more detectors configured to detect light spectra in response to the light beam, wherein the spectrometer sends a notification to the sample stage after a scan comprising an acceptable measure of quality has been acquired from the detected light spectra at a first location, and the sample stage is further configured to count the notifications and initiate movement of the sample stage to a second location when a count value reaches a pre-determined number.