Scientific instruments such as electron microscopes allow rapid development in many fields of science but are difficult to fully exploit. Even for experienced users, their internal state (shape of the electron beam), represented in conceptual models, remains fairly inaccessible. This prevents the operator from quickly understanding the complete causal link between the observed phenomenon and the resulting image. This paper investigates how a simulation and visualization application of such an instrument, may help users bridge the gap between their mental and the conceptual models of the instrument by displaying an approximation of its internal state in real time. This is supported by a study with 10 microscopists who had to perform a series of plausible tasks on the interface and answer questions. The study shows that users have a better understanding of the instrument’s inner state while using the user interface. These results will help software designers develop the next generation of scientific instrument tools.