With the particular interest of being implemented in cryptography, the recognition and analysis of image patterns based on Latin squares has recently arisen as an efficient new approach for classifying partial Latin squares into isomorphism classes. This paper shows how the use of a Computer Algebra System (CAS) becomes necessary to delve into this aspect. Thus, the recognition and analysis of image patterns based on these combinatorial structures benefits from the use of computational algebraic geometry to determine whether two given partial Latin squares describe the same affine algebraic set. This paper delves into this topic by focusing on the use of a CAS to characterize when two partial Latin squares are either partial transpose or partial isotopic.