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The use of a 1μm ion beam as a tomographic probe could constitute a powerful tool for displaying the 3D structure of samples a few tens or hundreds of micrometers thick in a nondestructive way. At the Centre d'Etudes Nucle´aires de Bordeaux-Gradignan (CENBG), Gradignan, France, ion beam microtomography has been developed for biomedical applications at the cell level. The internal structure of cancer cells has been explored using scanning transmission ion microscopy (STIM) tomography, giving access to the 3D distribution of mass density (in g/cm3) within the analyzed volume. The sole sample preparation required is cryofixation and freeze-drying, permitting under vacuum analysis. The combination of STIM and particle induced X-ray emission (PIXE) tomography is under progress with the aim of revealing the distributions and local concentrations of elements at the cell level.