Transmission electron microscopy (TEM) and scanning TEM (STEM) are indispensable tools for materials characterization. However, during a typical (S)TEM experiment, the sample is subject to a number of effects that can change its atomic structure. Of these, perhaps the least discussed are chemical modifications due to the non-ideal vacuum around the sample. With single-layer graphene, we show that even at relatively low pressures typical for many instruments, these processes can have a significant impact on the sample structure. For example, pore growth becomes up to two orders of magnitude faster at a pressure of ca. 10^{-6} mbar as compared to ultra-high vacuum (UHV; 10^{-10} mbar). Even more remarkably,the presence of oxygen at the sample also changes the observed atomic structure: When imaged in UHV, nearly 90% of the identifiable graphene edge configurations have the armchair structure, whereas armchair and zigzag structures are nearly equally likely to occur when the oxygen partial pressure in the column is higher. Our results both bring attention to the role of the often neglected vacuum composition of the microscope column, and show that control over it can allow atomic-scale tailoring of the specimen structure.
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