International audience•Proton micro-tomography experiments have been simulated using Geant4.•Geant4 gives access to information that is not possible to get from experiments.•A phantom of inertial confinement fusion target was constructed.•Accuracy of mass density images reconstructed by different methods was assessed.•Accuracy of the corrections implemented for X-ray attenuation was evaluated. The Geant4 toolkit was used to perform benchmark Monte Carlo simulations of proton micro-tomography imaging. A phantom of an inertial confinement fusion (ICF) target was designed, based on experimental data. Simulations of STIM (Scanning Transmission Ion Microscopy) and PIXE (Particle Induced X-ray Emission) tomography were performed. Quantitative ima...