Scanning transmission electron microscopy (STEM) combines the principles of transmission electron microscopy and scanning electron microscopy and can be performed on either type of instrument. Like TEM, STEM requires very thin samples and looks primarily at beam electrons transmitted by the sample. One of its principal advantages over TEM is in enabling the use of other of signals that cannot be spatially correlated in TEM, including secondary electrons, scattered beam electrons, characteristic X-rays, and electron energy loss.

Like SEM, the STEM technique scans a very finely focused beam of electrons across the sample in a raster pattern. Interactions between the beam electrons and sample atoms generate a serial signal stream, which is correlated with beam position to build a virtual image in which the signal level at any location in the sample is represented by the gray level at the corresponding location in the image. Its primary advantage over conventional SEM imaging is the improvement in spatial resolution.

Scattered beam electrons. Beam electrons may be elastically scattered by the nuclei of sample atoms. In a bulk specimen in a SEM, elastically scattered beam electrons that have been directed back out of the sample constitute the backscattered electron (BSE) signal. In STEM, transmitted beam electrons that have been scattered through a relatively large angle are detected using a high angle annular dark field (HAADF) detector.

X-ray microanalysis. Electrons bombarding the specimen cause it to emit X-rays whose energy is characteristic of the elemental composition of the sample. X-ray microanalysis uses an energy dispersive X-ray (EDX) spectrometer to count and sort characteristic X-rays according to their energy.

Wavelength dispersive X-ray (WDX) spectrometry measures and counts X-rays by their wavelength (a correlate of energy). A wavelength spectrometer uses a crystal or grating with known spacing to diffract characteristic X-rays.

Electron energy loss spectrometry (EELS) analyzes transmitted electrons to determine the amount of energy they have lost in interactions with the sample. It provides information about the interacting atoms, including elemental identity, chemical bonding, valence and conduction band electronic properties, surface properties, and element-specific pair distance distribution functions.