In 2016, CERN started investigating the use of GEMPix to measure the 3D energy deposition of a therapeutic ion beam in a water phantom, for medical imaging purposes. The GEMPix has been obtained by coupling two CERN-developed technologies, a triple GEM (Gas Electron Multiplier) detector and a Timepix ASIC for readout. The GEMPix has been developed by a CERN/INFN collaboration in the framework of the ARDENT Marie Curie proejct (2012-2016). The present work includes the development of the necessary software to drive the movement of the GEMPix in a dedicated water phantom, to acquire, normalise and elaborate the data, with the final goal of obtaining real-time imaging of the beam.