as you know there is an ADC (Analog to Digital Converter) in the output of the spectrometer to digitize the analog data output from the spectrometer which is actually the intensiy variation with the displacement in FTIR spectrometer , or the intensity corresponding to each wavelength incident on the array of the detectors in Dispersive spectroscopy,
that is why all measurements noise rms value , peak value,...etc are measured in counts , which are counts of the ADC , for example 16 bit ADC has a maximum level signal of 65,536 counts (2^16)