TEM and STEM are related techniques which can be considered as the most powerful tools to characterise nanomaterials and indispensable for nanotechnology. In both the cases, high energy electrons, incident on ultra-thin samples, allow for image resolutions that are on the order of 1-2 Angstroms. The electron beam travels through the specimen and, depending on the density of the material present, some of the electrons are scattered, while unscattered electrons hit a fluorescent screen at the bottom of the microscope, giving rise to a "shadow image" of the specimen with its different parts displayed in varied darkness according to their density. In the STEM mode, electrons pass through the specimen, but, as in scanning electron microscopy, the electron optics focus the beam into a narrow spot which is scanned over the sample in a raster. The rastering of the beam across the sample makes these microscopes suitable for analysis techniques such as mapping by energy dispersive X-ray (EDX) spectroscopy, electron energy loss spectroscopy (EELS) and annular dark field imaging (ADF). These signals can be obtained simultaneously, allowing direct correlation of image and quantitative data. By using a STEM and a high-angle detector, it is possible to form atomic resolution images where the contrast is directly related to the atomic number.

Traditionally, TEM/STEM have been mainly applied for imaging, diffraction, and chemical analysis of solid materials. For biological samples, cell structure and morphology is commonly determined whilst the localization of antigens or other specific components within cells is readily undertaken using specialised preparative techniques and, when required specific TEM cooling, holder.

A TEM can also be used to do Electron Tomography, which allows obtaining detailed three dimensional (3D) structural characterisation of 3D objects. This is accomplished by multiple views of the same specimen obtained by rotating the angle of the sample along an axis perpendicular to the beam. By taking multiple images of a single TEM sample at differing angles a set of images can be collected.

In the last few years, there has been a considerable revolution in electron microscopy with the arrival of aberration correctors for the objective lens with the consequent improvement in the attainable resolution limits. The obtainable resolution limit now lies at around 0,1 nm or better in both TEM and STEM, and the improved images from these aberration-corrected microscopes are opening up new avenues in the characterisation of materials.

Sample preparation is the most crucial part in TEM experiments. High quality TEM specimens have a thickness that is comparable to the mean free path of the electrons that travel through the samples, which may be only a few tens of nanometres. Preparation of TEM specimens is specific to the material under analysis and the desired information to obtain from the specimen. Sample preparation laboratories are equipped with the basic tools (diamond saw, polisher, dimpler, electropolisher, ultrasonic cutter, precision ion polishing system, gentle mill, plasma cleaner) commonly used in conventional chemical and mechanical thinning procedures.