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This work presents the use of a compact and cost-effective clock generator to be incorporated in a time-domain microwave medical device. We demonstrate the ability of the Adafruit Si5351 development board as an alternative to the currently used table-top Tektronix gigaBERT 1400. We demonstrate the ability to produce low-noise clock signals from the development board that allows for the proper triggering of both the impulse generator and high-speed oscilloscope in our system. The choice of the Adafruit Si5351 as a replacement clock is validated by the analysis of the resulting pulse stability. The paper also compares the shape of the waveforms produced by the system to verify that they remain unchanged.