OpenCFU is a completely open source lightweight application designed to enumerate clustered circular objects such as bacterial colonies. It can handle digital pictures as well as live stream from a video device/webcam. OpenCFU is cross-platform, fast, reliable and allows the user to implement intuitive filters.
Additional information is provided on the website: http://opencfu.sourceforge.net/
OpenCFU is published on PLoS ONE:
Opencfu works great.