A method of indexing atomic units of a crystal structure, characterized in that the method comprises the steps of: - acquiring an image of the crystal structure, the image representing a plurality of atomic patterns; - processing the acquired image to obtain a set of points, each point (P n) of the set of points being associated with an atomic pattern of the acquired image and each point of the set of points being located in a reference coordinate frame; - application of a triangulation algorithm to the set of points to obtain a triangular mesh, each vertex of a triangle (T n) of the triangular mesh being a point of the set of points, a particular point of the set of points being linked to a so-called adjacent point by one side of a triangle; - determination of the direction vectors ( A, B) of the crystal structure from the properties of the triangles of the triangular mesh, a direction vector defining a main direction of the crystal structure, an index being associated with each main direction; and, - indexing of each point of the set of points, by successive iterations starting from a point selected as the origin point (P 0) and whose indices along each of the main directions are zero, by selecting a point indexed at the preceding iteration as the central point (P c), by checking whether a neighbor point (P k) of said central point corresponds to a translation of the central point according to a translation vector equal to one of the direction vectors, or one of the opposite vectors thereof, and, if so, incrementing or decrementing, respectively, the index of the central point along the main direction associated with the translation vector so as to index said neighbor point from the indices of the central point. - acquiring an image of the crystal structure, the image representing a plurality of atomic patterns; - processing the acquired image to obtain a set of points, each point (P n) of the set of points being associated with an atomic pattern of the acquired image and each point of the set of points being located in a reference coordinate frame; - application of a triangulation algorithm to the set of points to obtain a triangular mesh, each vertex of a triangle (T n) of the triangular mesh being a point of the set of points, a particular point of the set of points being linked to a so-called adjacent point by one side of a triangle; - determination of the direction vectors ( A, B) of the crystal structure from the properties of the triangles of the triangular mesh, a direction vector defining a main direction of the crystal structure, an index being associated with each main direction; and, - indexing of each point of the set of points, by successive iterations starting from a point selected as the origin point (P 0) and whose indices along each of the main directions are zero, by selecting a point indexed at the preceding iteration as the central point (P c), by checking whether a neighbor point (P k) of said central point corresponds to a translation of the central point according to a translation vector equal to one of the direction vectors, or one of the opposite vectors thereof, and, if so, incrementing or decrementing, respectively, the index of the central point along the main direction associated with the translation vector so as to index said neighbor point from the indices of the central point.