A microscope system for obtaining a standardized quantitative measurement, of target sample data obtained from an intensity measurement, when a target sample is imaged by a microscope having an excitation light source, an optics means, an image capture means, and a data storage means, cooperatively arranged for obtaining an image of the target sample, the microscope system comprising: the microscope having the excitation light source, the optics means, the image capture means, and the data storage means, cooperatively arranged for obtaining the image of the target sample; means for obtaining for the excitation light source, a light source correction factor, comprising a calibration instrument and means for switching the calibration instrument into and out of an optical path to allow a relative light intensity measurement to be obtained substantially simultaneously with the target sample image; means for illuminating with the excitation light source the calibration instrument; wherein the calibration instrument comprises a calibration surface positioned along an optical path to substantially uniformly scatter illumination from the excitation light source toward the image capture means and further comprises a dichromatic mirror positioned to reflect illumination from the excitation light source along an optical path through the optics means toward the target sample and to transmit at least a portion of illumination from the target sample toward the image capture means, wherein the calibration surface temporarily blocks the optical path between the dichromatic mirror and the optics means during calibration and scatters a substantial portion of the reflected excitation light through the dichromatic mirror toward the detector; means for applying the light source correction factor to the target sample data, thereby obtaining standardized quantitative measured target sample data standardized with regard to temporal light intensity variability of the excitation light source. the microscope having the excitation light source, the optics means, the image capture means, and the data storage means, cooperatively arranged for obtaining the image of the target sample; means for obtaining for the excitation light source, a light source correction factor, comprising a calibration instrument and means for switching the calibration instrument into and out of an optical path to allow a relative light intensity measurement to be obtained substantially simultaneously with the target sample image; means for illuminating with the excitation light source the calibration instrument; wherein the calibration instrument comprises a calibration surface positioned along an optical path to substantially uniformly scatter illumination from the excitation light source toward the image capture means and further comprises a dichromatic mirror positioned to reflect illumination from the excitation light source along an optical path through the optics means toward the target sample and to transmit at least a portion of illumination from the target sample toward the image capture means, wherein the calibration surface temporarily blocks the optical path between the dichromatic mirror and the optics means during calibration and scatters a substantial portion of the reflected excitation light through the dichromatic mirror toward the detector; means for applying the light source correction factor to the target sample data, thereby obtaining standardized quantitative measured target sample data standardized with regard to temporal light intensity variability of the excitation light source.