Depending upon the microscope used and the preparation technique, an entire intact organism, or thin slices through the interior of the sample can be examined by electron microscopy. The electron beam can pass through very thin sections of a sample (transmission electron microscopy) or bounced off of the surface of an intact sample (scanning electron microscopy). Samples must be prepared prior to insertion into the microscope because the microscope operates in a vacuum. Biological material is comprised mainly of water and so would not be preserved, making meaningful interpretation of the resulting images impossible. For transmission electron microscopy, where very thin samples are required, the sample must also be embedded in a resin that can be sliced.

For scanning electron microscopy, a sample is coated with a metal (typically, gold) from which the incoming electrons will bounce. The deflected electrons...