1. A microscope system comprising: a microscope comprising a multi-channel image-acquisition sensor configured to acquire images of a specimen at a plurality of channels of respective wavelengths; and a controller configured to: read, for respective channels, contrast adjusting methods for the images acquired by the multi-channel image-acquisition sensor; generate data representing luminance histograms for the respective images acquired by the multi-channel image-acquisition sensor; and process the generated data to remove lower luminance sides of the respective luminance histograms in which luminance is equal to or less than predetermined thresholds separately set for the plurality of channels based on the contrast adjusting methods read, to thereby adjust contrasts of the images acquired by the multi-channel image-acquisition sensor.