If you have a good idea of where the circles should be I suggest dividing the original image into a grid of smaller images. Smaller images are easier to handle, and you have more control over what you are searching for. You can also do this "virtually" by defining an array of small ROIs (maybe overlapping slightly) and iterating the search over the array. This way you should know exactly which circle you are talking about when comparing measurements.
ciao,
Ziozio