STM is a surface sensitive technique, therefore proper storage of samples is a critical step before doing STM. When possible, we measure the samples in the STM right after deposition. If this is not an option, the samples can be stored in the glass bell jar chamber, under vacuum or controlled ambient.
Different gases can be mixed in. Oxides may not be preserved in oxygen poor athmosphere for a very long time, or the first atomic layers will become oxygen depleted. Oxides are very sensitive to contamination by water, therefore they should always be stored away in the bell jar, under dry and clean conditions!