The invention relates to a method and a system for central computer controlled execution of at least one test run in a scanning microscope, particularly a confocal microscope, wherein at least one first software module of an application software is tested. The invention achieves the aim by a network made of individual scanning microscope clients and a central server. The clients can be contacted via a network interface and are administered in a central directory in the server. The application software for the individual components of a scanning microscope is made of individual software modules, each associated with a potential test. In order to be able to perform the various tests, the scanning microscope clients have been equipped on the hardware side with additional sensors and components that allow various operating parameters to be determined.