A controller for a 3D observation apparatus performing 3D observation based on parallax using a plurality of optical systems includes the following sections. A start time acquisition section obtains a start time when energization of the 3D observation apparatus is started. An interrupted time acquisition section obtains an interrupted time when previous energization of the 3D observation apparatus is interrupted. A non-active time calculation section calculates a non-active time which is a period of time between the interrupted time and the start time. A determination section determines whether or not misalignment correction to correct misalignment of optical axes of the optical systems is necessary based on the non-active time.
