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We introduce an algorithm for determining scaling, rotation, and shift parameters of images in neutral-atom quantum computers. The algorithm includes noise suppression, Otsu binarization, contour search using Theo Pavlidis algorithm, and affine transformation via Coherent Point Drift (CPD) algorithm. CPD algorithm is enhanced for correspondence search between regular lattices and the entire process is implemented in C++ using Boost.GIL and Eigen libraries. The new algorithms are integrated into existing code to provide a faster and more accurate method for atom detection. Additionally, a method for refining atom recognition threshold is proposed.