Provided is a microscope system including a motor-driven stage on which is mounted a culture vessel containing one or more cell clusters, each including cells having a target molecule labeled with a fluorescent or luminescent chemical; a low-magnification-image acquiring unit that acquires low-magnification images of the cell clusters in the culture vessel mounted on the stage; a detecting unit that detects the position of each cell cluster in the culture vessel by analyzing the acquired low-magnification images; and a high-magnification-image acquiring unit that, after the detected position is aligned with the optical axis of an objective lens, acquires slice images of fluorescence or luminescence emitted from the cells forming the cell cluster at a higher magnification than the low-magnification-image acquiring unit at intervals along the optical axis while the stage and/or the lens is moved to change stepwise the distance between the lens and the cell cluster.