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An electron microscope was a microscope used to analyse samples of matter, often biological or chemical matter. (PROSE: Placebo Effect)
The pathologist, Doctor Carter, used his electron microscope to examine samples taken from the hand of Eldrad. The Fourth Doctor judged by the change in the electron charge that the hand was absorbing radiation. (TV: The Hand of Fear)
Monarch had a electron microscope aboard his spaceship. (TV: Four to Doomsday)
The Eighth Doctor had at least two electron microscopes in his TARDIS, along with a holographic magnifier, dimensional revisualiser and an antique brass microscope. (PROSE: The Dying Days, The Janus Conjunction)