1. A microscope system comprising: a microscope provided with a multi-channel image-acquisition unit that acquires images of a specimen at respective wavelengths; an adjustment-method storage portion that stores, for respective channels, contrast adjusting methods for the images acquired by the image-acquisition unit; and a contrast adjusting portion that adjusts, for the respective channels, the images acquired by the image-acquisition unit based on the contrast adjusting methods stored in the adjustment-method storage portion.