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Transmission electron microscopy accelerates electrons through a thin sample, then uses electron lenses to form an image or diffraction pattern. Elastic scattering encodes projected structure and potential; inelastic scattering carries excitation and chemical information. Thin specimens reduce unwanted multiple scattering and absorption, although coherent dynamical scattering can still matter in a crystal. High-resolution phase-contrast images depend on defocus and the transfer function as well as the specimen; they are not direct height maps.

The relativistic wavelength is $\lambda =h/\sqrt{2m_{e}eV[1+eV/(2m_e{c}^2)]}$. A shorter wavelength permits fine resolution but does not guarantee it. A schematic probe/image blur budget contains diffraction $\sim \lambda /\alpha$, spherical aberration $\sim C_s{\alpha }^3$ and chromatic aberration $\sim C_c\alpha \Delta E/E$, plus source size, instabilities, specimen motion and radiation damage. Optimizing the aperture angle balances these terms; increasing accelerating voltage can also alter damage and contrast.

Bright-field imaging accepts the central transmitted beam or its neighborhood. Regions that scatter electrons outside that acceptance can appear dark. Conventional dark-field imaging selects a diffracted beam. Annular dark-field electron imaging in a scanning TEM instead collects a range of scattered angles while a probe is scanned. A sufficiently high-angle detector often gives strong atomic-number sensitivity and more nearly incoherent contrast; thickness, channeling and detector geometry prevent a universal conversion of intensity to composition.

Electron energy loss spectroscopy measures energy lost by transmitted electrons. Core-ionization thresholds identify elements, while near-edge fine structure probes bonding and unoccupied states. At successive probe positions, one can record a spectrum image or form a map from a selected edge after background subtraction. Plural scattering, edge overlap, delocalization, specimen thickness and counting statistics limit the interpretation. Chemical specificity comes from excitation energies and spectral structure, not from brightness alone.

A development already established before this 2012 paper is aberration-corrected transmission electron microscopy: multipole correctors compensate leading lens aberrations, allowing useful larger angular acceptance and finer probes. Correction does not remove every chromatic, stability or specimen limit. A concrete application was atom-by-atom annular-dark-field analysis of monolayer boron nitride with substitutional defects, resolving chemical differences between sites in a nonuniform lattice.^[ref] Combining structural maps with spatially resolved core-loss spectra supplies another route to distinguish composition and bonding at interfaces. Both exploit a calibrated imaging or spectroscopy response rather than assuming every visible spot is chemically self-identifying.

A scanning transmission electron microscope makes an image by assigning a transmitted-electron signal to each position of a scanned probe. Its essential chain is electron source, probe-forming optics, scan system, thin specimen, transmitted-electron detectors and synchronized acquisition.

An electron gun and accelerating supply provide a stable beam of the chosen kinetic energy. Condenser lens optics and an aperture control probe current and convergence; the probe-forming objective lens focuses a small spot on the specimen. Alignment, focusing and astigmatism correction keep the probe usable across the field.

Scan coils deflect the probe in a raster. A stable specimen holder positions an electron-transparent region, and a high-vacuum column limits gas scattering and contamination. A bright-field transmission electron microscopy detector collects the central transmitted beam; an annular detector can select annular dark-field electron imaging, including high-angle annular dark-field imaging. Different angular selections give different contrasts, rather than a universal map of height.

Detector electronics, scan timing and a computer assign the collected signal to the corresponding image pixel. Spectrometers are useful additions but not essential to basic image formation. The post-specimen optics can adjust detector collection geometry; they do not set scan-image magnification in the same way as the projection lenses of conventional transmission imaging.