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This paper presents an automated cell contour visual measurement technique and a data synchronization mechanism for real-time, high-accuracy mechanical characterization of individual cells with micropipette aspiration. A computer vision tracking algorithm is developed for automatically measuring cell deformation parameters in real time (30 Hz) with a resolution down to 0.21 pixel, significantly enhancing the accuracy and efficiency of micropipette aspiration. To achieve a high characterization accuracy, the cell deformations and applied pressure changes are precisely synchronized using a data synchronization mechanism. Experimental results on both solid-like cells (interstitial cells) and liquid-like cells (neutrophils) quantitatively demonstrate that the visual tracking algorithm is capable of significantly increasing the efficiency and accuracy of micropipette aspiration. Among several characterized mechanical parameters, the viscoelastic properties of porcine aortic valve interstitial cells were, for the first time, quantified in this study.