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Training simulators that provide realistic visual and haptic feedback during cell indentation tasks are currently investigated. Complex cell geometry inherent to biological cells and intricate mechanical properties drive the need for precise mechanical and numerical modeling to assure accurate cell deformation and force calculations. Advances in alternative finite-element formulation, such as the mass-tensor approach, have reached a state, where they are applicable to model soft-cell deformation in real time. The geometrical characteristics and the mechanical properties of different cells are determined with atomic force microscopy (AFM) indentation. A real-time, haptics-enabled simulator for cell centered indentation has been developed, which utilizes the AFM data (mechanical and geometrical properties of embryonic stem cells) to accurately replicate the indentation task and predict the cell deformation during indentation in real time. This tool can be used as a mechanical marker to characterize the biological state of the cell. The operator is able to feel the change in the stiffness during cell deformation between fixed and live cells in real time. A comparative study with finite-element simulations using a commercial software and the experimental data demonstrate the effectiveness of the proposed physically based model.