The scanning helium microscope (SHeM) is a form of microscopy that uses low-energy (5–100 meV) neutral helium atoms to image the surface of a sample without any damage to the sample caused by the imaging process. Since helium is inert and neutral, it can be used to study delicate and insulating surfaces. Images are formed by rastering a sample underneath an atom beam and monitoring the flux of atoms that are scattered into a detector at each point.

The technique is different from a scanning helium ion microscope, which uses charged helium ions that can cause damage to a surface.

Microscopes can be divided into two general classes: those that illuminate the sample with a beam, and those that use a physical scanning probe. Scanning probe microscopies raster a small probe across the surface of a sample and monitor the interaction of the probe with the sample. The resolution of scanning probe microscopies is set by the size of the interaction region between the probe and the sample, which can be sufficiently small to allow atomic resolution. Using a physical tip (e.g. AFM or STM) does have some disadvantages though including a reasonably small imaging area and difficulty in observing structures with a large height variation over a small lateral distance.

Microscopes that use a beam have a fundamental limit on the minimum resolvable feature size, ${\displaystyle d_{\text{A}}}$, which is given by the Abbe diffraction limit,

where ${\displaystyle \lambda }$ is the wavelength of the probing wave, ${\displaystyle n}$ is the refractive index of the medium the wave is travelling in and the wave is converging to a spot with a half-angle of ${\displaystyle \theta }$. While it is possible to overcome the diffraction limit on resolution by using a near-field technique, it is usually quite difficult. Since the denominator of the above equation for the Abbe diffraction limit will be approximately two at best, the wavelength of the probe is the main factor in determining the minimum resolvable feature, which is typically about 1 μm for optical microscopy.

To overcome the diffraction limit, a probe that has a smaller wavelength is needed, which can be achieved using either light with a higher energy, or through using a matter wave.

X-rays have a much smaller wavelength than visible light, and therefore can achieve superior resolutions when compared to optical techniques. Projection X-ray imaging is conventionally used in medical applications, but high resolution imaging is achieved through scanning transmission X-ray microscopy (STXM). By focussing the X-rays to a small point and rastering across a sample, a very high resolution can be obtained with light. The small wavelength of X-rays comes at the expense of a high photon energy, meaning that X-rays can cause radiation damage. Additionally, X-rays are weakly interacting, so they will primarily interact with the bulk of the sample, making investigations of a surface difficult.

Matter waves have a much shorter wavelength than visible light and therefore can be used to study features below about 1 μm. The advent of electron microscopy opened up a variety of new materials that could be studied due to the enormous improvement in the resolution when compared to optical microscopy.