# Medical Applications of the GEMPix
## 2 The GEMPix
This mode is typically used for 3D reconstruction of a track inside the detector. The readout mode can be chosen for each pixel individually, such that a combined ToT and ToA analysis of a charge cluster becomes possible when using a mixed mode by operating some pixels in ToA mode and the rest of the pixels in ToT mode. The Timepix ASICs are read out by the FITPix, an FPGA based module shown in Figure 1 [35] using the Pixelman software [36]. This software, developed by the University of Prague, is able to save the time and charge information of each pixel within the preset time interval in matrix form, showing the image obtained online and saving the data to a  
Figure 3: The Timepix chip with the standard silicon sensor on top. The GEMPix uses four ‘naked’ Timepix ASICs, i.e., without the silicon sensor chip (source: CERN). Figure 2: (**Left**) magnified image of a GEM foil. (**Centre**) scheme of a typical triple GEM in the GEMPix detector and the electric transport fields: drift field (ED), transfer fields (ET) and induction field (EI). (**right**) electron multiplication (source: CERN). file. It is also possible to use an online cluster analysis in order to write a file with the list of reconstructed pixel clusters, reporting for each one the main information such as start time of the event, the total number of clusters, and for each of them the total charge, some geometric parameters and the position. The GEMPix can be assembled with different drift gap sizes according to the type of particle to be detected. In the case of charged particles, a few millimeters are sufficient to produce a dozen electrons distributed along the gap, which are sufficient to generate a detectable signal. There are two possible configurations visible in Figure 4: one in which the particle enters perpendicularly to the GEM foils (\"head-on\") and one in which the particle enters parallel to them (\"side-on\"). In the second case, it is possible to expand the drift area up to a few centimeters in order to create a small TPC with the possibility to reconstruct the particle track in three dimensions, as for example used in proton tomography (Section 5). In the case of soft X-rays, a gap of about 1 cm is preferred, both to increase the detection efficiency and to contain all the tracks of the primary electron produced. In addition, metal layers suitably designed for the detection of gamma rays can be inserted in the drift area. Recently, thin layers of B4C have been used for the detection of thermal neutrons: the lithium ion and alpha particle produced in the \({}^{10}\)B(n,\(\alpha\)) reaction strongly ionize the gas in the drift zone, allowing a good discrimination from the gamma signal. In some applications with high intensity beams or highly ionizing particles, it is possible to reduce the detector configuration to two GEM foils with the advantage of a lower lateral diffusion of the electron cloud and therefore of a better spatial resolution (measurements with only two GEMs turned on are described in Section 3). A detailed study on the gas mixture has been performed in the past [37] showing that a time resolution of better than 5 ns is achieved with CF4 and iso-C4H10 based gas mixtures, considerably improving the results obtained with the standard Ar/CO2 (70/30) mixture. Regarding the discharge probability, the use of a small fraction of iso-C4H10 or a large amount of CF4 results in a very stable detector operation. Therefore, an Ar/CO2/CF4 (45/15/40) gas mixture is often used with the GEMPix detector. The HVGEM [32], designed at the Frascati National Laboratories (LNF) of the National Institute of Nuclear Physics (INFN) in Italy, is built with seven floating power supplies with a maximum of 1200 V each, controlled via CANbus and a LabVIEW based software for voltage settings and current monitoring. In this way, each GEM foil has its own power supply allowing a safe operation of the detector, avoiding dangerous discharges versus the front-end electronics.