The atomic beam is formed through a supersonic expansion, which is a standard technique used in helium atom scattering. The centreline of the gas is selected by a skimmer to form an atom beam with a narrow velocity distribution. The gas is then further collimated by a pinhole to form a narrow beam, which is typically between 1–10 μm. The use of a focusing element (such as a zone plate) allows beam spot sizes below 1 μm to be achieved, but currently still comes with low signal intensity.
The gas then scatters from the surface and is collected into a detector. In order to measure the flux of the neutral helium atoms, they must first be ionised. The inertness of helium that makes it a gentle probe means that it is difficult to ionise and therefore reasonably aggressive electron bombardment is typically used to create the ions. A mass spectrometer setup is then used to select only the helium ions for detection.
Once the flux from a specific part of the surface is collected, the sample is moved underneath the beam to generate an image. By obtaining the value of the scattered flux across a grid of positions, then values can then be converted to an image.
The observed contrast in helium images has typically been dominated by the variation in topography of the sample. Typically, since the wavelength of the atom beam is small, surfaces appear extremely rough to the incoming atom beam. Therefore, the atoms are diffusely scattered and roughly follow Knudsens Law [citation?] (the atom equivalent of Lamberts cosine law in optics). However, more recently work has begun to see divergence from diffuse scattering due to effects such as diffraction and chemical contrast effects. However, the exact mechanisms for forming contrast in a helium microscope is an active field of research. Most cases have some complex combination of several contrast mechanisms making it difficult to disentangle the different contributions.
Combinations of images from multiple perspectives allows stereophotogrammetry to produce partial three dimensional images, especially valuable for biological samples subject to degradation in electron microscopes.