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The repetitive contraction of the myotube has been measured by the local movement of micro-markers on the thin film of the scaffold during the electric stimulation in vitro. The scaffold is made of the thin polydimethylsiloxane film (6 μm thickness), of which the back side has an arrangement of micro-protrusions (4 μm diameter, 2 μm height, and 30 μm interval) made using the photolithography technique. Mouse myoblasts (C2C12) were seeded on the film at the counter surface to the protrusions at the density of 50000 cells/cm2. The cells differentiated on the scaffold into myotubes over 12 days in a medium containing 10% FBS (fetal bovine serum) and 1% penicillin/ streptomycin in the incubator. The electric pulses (30 V amplitude, 1 s pulse cycle, and 1 ms pulse width) were applied between electrodes of titanium wire dipped in the medium. The contraction of the myotube was observed by a microscope through the transparent scaffold. The experimental results show that the amplitude of the cyclic variation of the distance between micro-markers relates to the distance and the alignment. The designed scaffold can be applied to analyze the local contractile movement of the layer of myotubes in vitro.