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Orientation control of biological cells under inverted microscopes is important for cell birefringent imaging and micromanipulation. Taking our microrobotic mouse embryo injection research as an example, this paper presents a cell orientation control system operated under inverted microscopes. A compact motorized rotational stage for inverted microscopy was developed for orienting the polar body of mouse embryos away from the injection site to avoid damage of cellular organelles. An in-house developed microdevice was used for immobilizing many cells into a regular pattern. The polar body is tracked by a visual tracking algorithm with a translation-rotation-scaling motion model, providing image position feedback to an image-based visual servo controller that is responsible for online calibration of coordinate transformation during visually servoed orientation of the first embryo. High-speed, automatic cell orientation is then conducted on other embryos in the same batch of immobilized embryos through coordinate transformation and 3-DOF closed-loop position control. Experimental results demonstrate that the cell-orientation system is capable of orienting mouse embryos at a high speed of 720°/s with an accuracy of 0.24°.