Proper alignment of the end-effector is a critical procedure that determines the success of micromanipulation, such as robotic cell manipulation. Presently, end-effector alignment is performed manually and suffers from large misalignment error and inconsistency. Manual alignment often undesirably moves the end-effector (e.g., a glass micropipette) out of the limited field of view under microscopy and risks breaking the fragile end-effector. This article presents automated end-effector alignment in robotic micromanipulation. A rotational degree of freedom was added to a standard micromanipulator with translational degrees of freedom. The kinematic model of end-effector’s rotation was established, and the unknown model parameters were calibrated. To accommodate model uncertainty and parameter variations, a sliding mode controller was designed to achieve end-effector alignment. Experimental results demonstrate that the robotic alignment technique achieved an accuracy of 0.5 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\pm 0.3^{\circ }$</tex-math></inline-formula> and a time cost of 17.9 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\pm$</tex-math></inline-formula> 7.3 s, both significantly less than manual alignment. The developed controller based on kinematic modeling and sliding mode control achieved a higher success rate and significantly less time cost for end-effector alignment than the PID controller. Standard micropipettes were used as the end-effectors for sperm immobilization and oocyte penetration, important procedures in cell surgeries. The success rate of sperm immobilization was 98% by robotic micropipette alignment, higher than the success rate of 90% by manual alignment. Oocyte deformation before penetration was 28.1 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\pm$</tex-math></inline-formula> 7.5 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\mu$</tex-math></inline-formula> m by robotic end-effector alignment, significantly less than the deformation of 54.5 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\pm$</tex-math></inline-formula> 13.2 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\mu$</tex-math></inline-formula> m by manual alignment.
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