A microscope system comprising: a stage on which a sample is mounted and that is movable in a direction perpendicular to an observation optical axis; a position detecting unit (9, 17) that detects a position of the stage; a speed detecting unit (9, 18) that detects a moving speed of the stage; an image acquisition unit that is configured to capture an image of the sample on the stage when the position of the stage is a position that is suitable for image capturing; and an image generating unit that joins the image of the sample newly obtained by the image acquisition unit with a joined image stored in a storage unit to generate a new joined image, the storage unit being configured to store a joined image generated by the image generating unit and to update the stored joined image when a new joined image is sent thereto from the image generating unit; characterized in that the microscope system further includes: a determination unit that determines, on the basis of the position of the stage detected by the position detecting unit (9, 17), whether the position of the stage is a position that is suitable for image capturing by the image acquisition unit; a notifying unit that, when it is determined as a result of the determination by the determination unit that the position of the stage is suitable for image capturing, issues a notification to the user to that effect; and a control unit that controls the image generating unit so as to join the image newly obtained by the image acquisition unit when the moving speed of the stage detected by the speed detecting unit (9, 18) is at or below a prescribed threshold, in the state where it is being notified by the notifying unit that the position of the stage is suitable for image capturing, with the joined image stored in the storage unit to generate the new joined image. a stage on which a sample is mounted and that is movable in a direction perpendicular to an observation optical axis; a position detecting unit (9, 17) that detects a position of the stage; a speed detecting unit (9, 18) that detects a moving speed of the stage; an image acquisition unit that is configured to capture an image of the sample on the stage when the position of the stage is a position that is suitable for image capturing; and an image generating unit that joins the image of the sample newly obtained by the image acquisition unit with a joined image stored in a storage unit to generate a new joined image, the storage unit being configured to store a joined image generated by the image generating unit and to update the stored joined image when a new joined image is sent thereto from the image generating unit; a determination unit that determines, on the basis of the position of the stage detected by the position detecting unit (9, 17), whether the position of the stage is a position that is suitable for image capturing by the image acquisition unit; a notifying unit that, when it is determined as a result of the determination by the determination unit that the position of the stage is suitable for image capturing, issues a notification to the user to that effect; and a control unit that controls the image generating unit so as to join the image newly obtained by the image acquisition unit when the moving speed of the stage detected by the speed detecting unit (9, 18) is at or below a prescribed threshold, in the state where it is being notified by the notifying unit that the position of the stage is suitable for image capturing, with the joined image stored in the storage unit to generate the new joined image.