A Geant4 simulation of X-ray emission for three-dimensional proton imaging of microscopic samples

•PIXE tomography distributions of element content are obtained for thick samples.•Corrections for X-ray attenuation are modeled in the reconstruction code.•The accuracy of the reconstructed tomographic images is evaluated using Geant4.•A good agreement is obtained (accuracy ≤4% for phosphorus).•Geant4 provides data that cannot be obtained experimentally.