Bacterial colony forming unit (CFU) counting is a tedious task mostly done by humans. Procedure is error prone, time-consuming and laborious. In this paper we present a semi-automatic prototype system for CFU counting. The developed prototype consist of a hardware (area scan camera with LED light source) and C#-based desktop application. The application enables manual, semi-automatic and automatic CFU counting. Automatic CFU counting is based on Hough transform for circles. Obtained results can be user-corrected for better accuracy. In the experimental analysis, the developed application is evaluated on the synthetic CFU images. The results include time and counting performance measurements compared with the manual count. The results show that semi-automatic counting procedure can save on average 45% of counting time compared to manual count with the same counting accuracy. The automatic CFU counting on average has precision of 97% and recall of 82%.