The CELLION project is directed towards the studies on cellular response to targeted single ions. This paper gives an account of the modifications made at the Lund sub-micron beam line in order to create a Single Ion Hit Facility for biological applications within the CELLION project. The most relevant new feature is the specially developed software used to locate the cells. A program for cell recognition and localization that gives the coordinates of the centre of the cells has been designed. The recognition is made online. A picture taken by a microscope is used as input parameter for the recognition program. Using V79 Chinese hamster cells, the recognition procedure can be done in less than 0.5 s for a picture size of 800 x 600 pixels with approximately 96% efficiency. This paper also reports target accuracy test results and the first non-targeted irradiation procedure performed at the Lund sub-micron beam line. (c) 2007 Elsevier B.V. All rights reserved.