Did you follow the five steps outlined at http://imagej.net/Segmentation ?
Preprocess – maybe/probably not necessary for this data since it is very clean.
Threshold (shift+T) – you just need to convert to 8-bit or split channels first to do this. Or use the Color Threshold plugin. (Press L to launch Command Finder for easy access to commands.)
- Create Mask
- Analyze Particles
Measure (with your original image selected!)
Step 4, Analyze Particles, is really important to split up the foreground from a single monolithic blob into your individual objects. You will end up with all your objects in the ROI Manager afterwards as long as you check the “Add to manager” option. Then for Step 5 you click the ROI Manager’s Measure button to measure each object separately.
See also info about the Macro Recorder to create a macro for reproducing these steps repeatedly, as well as the Batch page for more tips.