Using a scanned, focused MeV ion beam, the techniques of ion beam analysis can be used to obtain images showing two-dimensional elemental distributions. This technique of nuclear muscopy is important in applications where the distribution of elements within a sample must be related to optical or electron images showing the structure or functional organisation of the sample. With the techniques available at present, spatial resolutions of 0.5 μm can be achieved at currents allowing PIXE analysis of trace elements at the ppm level. The simultaneous use of particle backscattering analysis and secondary-electron imaging allows the light elements and the surface topography of the sample to be determined. In some cases, nondestructive three-dimensional elemental analysis can be carried out. This paper reviews the techniques and describes two applications in semiconductor physics and microbiology carried out using the facility at Oxford.