1. A microscope system, comprising: a stage on which a specimen is placed; a division unit which divides the specimen into a plurality of sections; a capture condition setting unit which sets a capture condition used when capturing the specimen; a capture unit which captures the specimen based on the capture condition set by the capture condition setting unit, and which acquires an image of each section of the specimen; a capture parameter acquisition unit which acquires, for each section of the specimen, a corresponding capture parameter set when the image of each section was acquired; an image composition unit which combines images of adjacent sections acquired by the capture unit to obtain a composite image; an image display unit which displays the composite image; and an image processing unit which performs a first image process on the composite image when the capture parameters acquired by the capture parameter acquisition unit are different for each of the sections, wherein in the first image process, processing is performed to represent the composite image as if it were obtained by combining images of adjacent sections which were acquired using a same predetermined capture parameter.