findTransformECC() With Multiple warpMatrix's

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I am exploring using findTransformECC() in my application where there can be multiple matches between template image in a larger candidate image (e.g., template is a circular ball and candidate is a repeating pattern of those circular balls). Would you share if you know there is a way to find all the matches (i.e., multiple warpMatrix's).

I initially selected findTransformECC() as the method of my choice as it is a pixel intensity based and offers an option for input mask array. However I am open to other methods.