The present invention relates to a compact motorized rotational stage for microscopy applications and control methods for automated sample orientation/rotation. The rotational stage includes a motor, a rotational motion transmission mechanism, and a rotating sample holder for accommodating a holding device such as glass slides/Petri dishes of different sizes. Mouse embryos are used as an example to explain the control methods. A pattern recognition utility was developed for identifying mouse embryo structures. The transformation between the holding device rotational coordinate frame and the translational positioning stage coordinate frame is calibrated during image-based visual servo control. The polar body of an embryo is oriented through purely image-based visual servo control or through coordinate transformation and closed-loop position control.