Scanning helium microscopy (SHeM) is a novel form of microscopy that uses low energy (5-100 meV) helium atoms to image the surface of a sample. Since helium is inert and neutral, it can be used to study delicate and insulating surfaces, but that also means it can be difficult to manipulate for focussing and detection. The first reflection mode helium images were recently demonstrated using a pinhole to form a narrow beam of helium, but without any focussing of the beam the low signal levels pose a significant challenge. This thesis aims to advance the field by describing how to improve the instrumentation for a helium microscope and how both previously observed and novel contrast is formed in images. The thesis begins with an introduction in chapter 1 to motivate the development of a helium microscope. Chapter 2 contains a literature review of beam formation methods and successful implementations of helium microscopy to date. In chapter 3, the design of the scanning helium microscope is explained, with a description of how images of a surface can be formed with an atom beam. The key aspects of the machine are provided, including a new sample stage that uses a magnetically assisted kinematic mount and measurements of the size of the helium source. When using a pinhole to collimate the beam, the quality and resolution of images are largely determined by the performance of the detector. In chapter 4, the design, implementation and properties of a new helium detector that has both a high efficiency and low background are detailed. The detector is comprised of a solenoidal ioniser, magnetic sector for mass selection and finally a conversion dynode and electron multiplier for measuring the ion current. In chapter 5, the origins of the observed contrast in images from a scanning helium microscope are discussed. For rough surfaces, the helium atoms are diffusely scattered from the surface and the resulting contrast mechanisms are investigated. The second half of the chapter focusses on new contrast mechanisms. By using a mixed gas beam, it is possible to simultaneously probe a surface with atoms at different energies and wavelengths, and the first such images are presented. It is well known that atom beams will diffract from well-ordered surfaces, and diffraction contrast on LiF is explicitly shown to be possible for the first time with a scanning helium microscope. Finally, the optimum geometry to maximise the flux using either a pinhole or zone plate to form the beam is investigated by performing a constrained optimisation in chapter 6. The source properties must also be included due to the strong chromatic aberrations present when using a zone plate. It is shown that the pinhole produces the largest flux for large helium spot sizes, but for small spot sizes the zone plate gives the highest flux and therefore the best signal to noise ratio in images, thus indicating the direction for future research.