In recent years, a single ion hit facility has been constructed at the IFJ ion microprobe. The setup is used for the precise irradiations of living cells by a controlled number of ions. Investigations of such type have two very important requirements: (1) cells must be examined in their natural state and environment (i.e. without previously being killed, preferentially neither fixed nor stained) and (2) the possibility of automatic irradiation of large number of cells (including computer recognition of cells positions) must be provided. This work presents some of the crucial features of the off-line and on-line optical systems, including self-developed software responsible for automatic cell recognition.