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Not sure OpenCV has feature detectors or descriptors for your 3d adjacency data. Have you looked at 3d descriptors like GASD ( or LFSH( These articles also discuss matching for registration. Once you find appropriate features, you should be able to use OpenCV's FLANN for matching. If you can represent the features or descriptors as integral data, you may be able to use hashing for fast matching/lookup. Please let us know what you come up with.