Hi selim,
I've actually worked on a similar problem of trying to match irregular shapes from a pattern of other shapes. (In my case, I was trying to identify axons on stained histology slides, but the principle is the same). I (and the rest of the Answers) community would be happy to offer some advice, but one thing that would help is a larger training set. Can you post a larger number of shapes that you want to match (say 20 or so)? That would give us a sense of the variation between matching shapes. Even better, can you post an image containing both shapes you want to match as well as those you wish to reject?
Thanks, Matt
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