The present invention provides a control method for a microscope apparatus, comprising: a first step for recognizing a type of a specimen retention member retaining a specimen; a second step for obtaining a first image including the whole image of a specimen retention member showing a picture of the entirety of the specimen retention member and an image of the specimen, and obtaining a second image including only the whole image of the specimen retention member in accordance with the type of the specimen retention member; and a third step for obtaining a macro observation image with a self fluorescence removed except for the specimen based on the first image and second image.