Microscopes can be separated into several different classes. One grouping is based on what interacts with the sample to generate the image, for example; light or photons (optical microscopes) or electrons (electron microscopes).

Wide field optical microscopes and transmission electron microscopes both use the theory of lenses in order to magnify the image generated by the passage of a wave transmitted through the sample, or reflected by the sample. The waves used are electromagnetic (in optical microscopes) or electron beams (in electron microscopes). Resolution in these microscopes is limited by the wavelength of the radiation used to image the sample, where shorter wavelengths allow for a higher resolution.

Scanning optical and electron microscopes use lenses to focus a spot of light or electrons onto the sample then analyse the reflected or transmitted waves. The point is then scanned over the sample to analyse a rectangular region. Magnification of the image is achieved by displaying the data from scanning a physically small sample area on a relatively large screen. These microscopes have the same resolution limit as wide field optical and electron microscopes.