  Transmission electron microscopy (TEM) is carried out in vacuum to minimize
the interaction of the imaging electrons with gas molecules while passing
through the microscope column. Nevertheless, in typical devices, the pressure
remains at 10^-7 mbar or above, providing a large number of gas molecules for
the electron beam to crack, which can lead to structural changes in the sample.
Here, we describe experiments carried out in a modified scanning TEM (STEM)
instrument, based on the Nion UltraSTEM 100. In this instrument, the base
pressure at the sample is around 2x10^-10 mbar, and can be varied up to 10^-6
mbar through introduction of gases directly into the objective area while
maintaining atomic resolution imaging conditions. We show that air leaked into
the microscope column during the experiment is efficient in cleaning graphene
samples from contamination, but ineffective in damaging the pristine lattice.
Our experiments also show that exposure to O2 and H2O lead to a similar result,
oxygen providing an etching effect nearly twice as efficient as water,
presumably due to the two O atoms per molecule. H2 and N2 environments have no
influence on etching. These results show that the residual gas environment in
typical TEM instruments can have a large influence on the observations, and
show that chemical etching of carbon-based structures can be effectively
carried out with oxygen.
