A microscopy system comprises a microscope configured to capture raw data and a computing device configured to derive at least one microscope image from the raw data and to run a processing program for processing the microscope image. The computing device is configured to first supply a microscope image which is to be processed with the processing program to a checking program, which checks the supplied microscope image with respect to an evaluation criterion predefined for the processing program. The microscope image is only transmitted to the processing program in the event of a positive checking result.