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In this paper, we study the effect of acoustic agitation on the penetration force for microinjections in Drosophila embryos for genome-wide RNA interference (RNAi) screens, using an integrated optical MEMS force encoder for in vivo characterization of the dynamic penetration forces. Two modes of operation are investigated. In the first mode of operation, the injector is brought into contact and acts on the embryo with a fixed force, and the vibration amplitude of the microinjector is increased till penetration occur. We observed a linear decrease in the penetration force of 1.6 μN with every 0.1 m/s tip velocity increase. In the second mode of operation, the vibration amplitude is kept constant and the injector is pushed into the embryo until penetration. We simulate the optical force encoder eigenmodes and measure the injection force over the frequency range from 0 to 16 kHz with actuation voltages up to 150V. Among the eight encoder eigenmodes with resonant frequency up to 16 kHz, the longitudinal vibration along the injector is shown to dominate the force reduction at 14 kHz. Two other modes, both involving significant out-of-plane injector motion, reduce the penetration force by 52% around 3.1 kHz. The average penetration force is calculated based on injections into multiple embryos for each experimental condition. For each microinjection, the peak (or average) penetration force can be derived from the peak (or average) relative displacement of the two gratings upon penetration. The achieved minimum peak penetration force was 15.6 μN (∼29.7% of the static penetration force), while the minimum average penetration force was 2.7 μN (5.1% of the static penetration force).