Using stereo endoscopes for 3D reconstruction in minimally invasive surgery, the calibration of the stereo system is required. Since calibration in general and of medical endoscopes in particular is a well discussed topic, this publication will focus on the user experience in the operating room. To enable the medical personnel in performing the calibration, a guided process using an augmented camera image has been developed and implemented on the basis of the Robot Operating System framework. A similarly guided accuracy check allows the user to determine beforehand if a calibration is necessary.The method is tested by performing multiple calibrations on two different stereo endoscopes. It is shown, that the accuracy check and calibration can be completed in around 2 minutes. The resulting calibration parameters for one endoscope are analyzed in terms of temporal stability. Additionally, the self-heating that occurs after the system starts is examined. It is shown that short- and long-term effects impact the stereo system stability and that regular re-calibrations might be required for use in 3D reconstruction.