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Electron microscopy images are interference patterns and can generally not be interpreted in a straight forward manner. Typically, time consuming numerical simulations have to be employed to separate specimen features from imaging artifacts. Directly comparing numerical predictions to experimental results, realistic simulation box sizes and varying imaging parameters are needed. In this work, we introduce an accelerated multislice algorithm, named STEMcl, that is capable of simulating series of large super cells typical for defective and amorphous systems, in addition to parameter series using the massive parallelization accessible in today’s commercial PC-hardware, e.g. graphics processing units (GPUs). A new numerical approach is used to overcome the memory constraint limiting the maximum computable system size. This approach creates the possibility to study systematically the contrast formation arising by structural differences. STEM simulations of structure series of a crystalline Si and an amorphous CuZr system are presented and the contrast formation of vacancies/voids are studied. The detectability of vacancies/voids in STEM experiments is discussed in terms of density changes.