The present invention concerns a method, an arrangement, and a software program for controlling analytical and adjustment operations of a microscope. The arrangement has an electronic acquisition system (50) which converts the electrical signals coming from the detectors (19) into digital signals and preprocesses them. A PC (34) receives the digital signals from the electronic acquisition system (50) and identifies from the digital signals a graphical depiction. On a display (27), the graphical depiction is displayed and moreover the user is offered the opportunity to select adjustment functions. An input unit (33), with which selection of the adjustment functions and selection of at least one structure of interest can be achieved, is provided for selection. An electronic control system (67), with which the adjusting elements of the microscope can be controlled, is connected to the PC (34).