The PTB microbeam is routinely used for the irradiation of living cells using protons (1-20 MeV) and alpha particles (1-28 MeV). The beam diameter is approximately 2 microm (fwhm), achieved by focussing, resulting in an excellent energy resolution and practically no scattered particles. Recently, an electrostatic beam scanner was added to the facility which allows targeting of each cell within 1 ms. This and other improvements led to an increase in the experimental speed of the system to a maximum of 50,000 cells per hour including all experimental steps. To improve the versatility of the facility further, a module for automatic quantification of immunocytochemical staining was implemented. This allows the analysis of protein activation, taking into account the positional information of the irradiation run.