Scanning transmission electron microscopes are the tools of choice for material science research, since they provide information on the internal structure of a wide range of specimens. These sophisticated machines are operated manually by skilled technicians, who execute complex and repetitive procedures, such as measuring nano-particles, using mainly visual feedback. Hence, there is a need for new global control strategies to automate these procedures. These strategies, however, must be based

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... n a firm understanding of the microscopes from the system theoretical perspective. To the best of our knowledge, such perspective is lacking in the literature. Thus, it is provided here through a new modeling framework that facilitates the future development of global control strategies. The paper also aims to introduce scanning transmission electron microscopy as an important and untapped area of application for control engineers.