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They are very expensive to initially purchase, and to maintain, after initial set-up costs.
They are very large, and cumbersome, taking up a whole room.
They are dynamic in their operation (this means that they require extremely stable high
voltage supplies, stable currents to each electromagnetic coil, vacuum systems which are
expensive to maintain and a cooling water supply circulation through the lenses and pumps.)
Electron microscopes are also very sensitive to vibration, and external magnetic fields,
meaning that they can be easily damaged, thus, requiring the construction of additional
rooms, with special services, in order to contain them.
Large amounts of training are required, in order to operate an electron microscope, and
thus, it is considered a specialised skill.
Because the samples must be viewed in a vacuum, the preparation of said samples often
requires lengthy, difficult techniques, to ensure that the sample can withstand the
conditions inside the microscope.