1. Open picture in Image J.
2. Go to process and scroll down to binary.
3. Click make binary/threshhold. (The terminology depends on the version you are running.)
4. Use the circle tool or the freehand tool to outline the area in which you wish the colonies to be counted.
5. Go to analyze and click analyze particles. Check Display Results, Clear Tables, and Summarize.
6. Click ok and a window will appear displaying how many particles are in the given area.
Directions taken from Fred Hutchinson Cancer Research Center.