[imagej]how to count dots on an image

Two steps:
1. using a threshold to convert your image into binary form (positive + negative)

 Image  ▶ Adjust  ▶ Threshold. 
check "dark background"
Drag the bars so that the thresholds let the particles/dots stand out while leaving no background smears there

2. If your dots have overlapping groups, force them to separate:
Process  ▶ Binary  ▶ Watershed.

3. Analyze Particles
size: 0-infinity or leave blank
More stringent: 10-infinity 
Analyze  ▶ Analyze particles
Show:  -> Eclipse
check display results and summarize




reference:
http://imagej.net/Particle_Analysis