Stirling micro coolers, such as the K508 from Ricor, are useful components of scientific instruments when there is a need to remove modest amounts of heat (∼1/2 W) at liquid nitrogren temperatures with an input power of less than 10 W. The action of the cooler can, however, couple noise into sensitive detectors through a variety of mechanisms such as electromagnetic interference, mechanical vibration, and small temperature fluctuations. We report on successful noise-mitigation strategies for our application, an InSb diode for detecting light at 2.4 microns. The largest benefit was obtained by sychronizing the integration times with the position of the piston in the micro cooler. The piston position was determined using a hall-effect rotor position sensor in the driving motor.