Robustly find N circles with the same diameter: alternative to bruteforcing Hough transform threshold

Question

I am developing application to track small animals in Petri dishes (or other circular containers). Before any tracking takes place, the first few frames are used to define areas

Answer 1

Within the current algorithm, the biggest thing that sticks out is the for(int t=5; t<400; t=t+2) loop. Trying recording score values for some test images. Graph score(t) versus t. With any luck, it will either suggest a smaller range for t or be a smoothish curve with a single maximum. In the latter case you can change your loop over all t values into a smarter search using Hill Climbing methods.

Even if it's fairly noisy, you can first loop over multiples of, say, 30, and for the best 1 or 2 of those loop over nearby multiples of 2.

Also, in your score function, you should disqualify any results with overlapping circles and maybe penalize overly spaced out circles.