An image alignment tool is described for adjusting the alignment of a grid with an image. An initial grid aligner determines an initial, approximately aligned, position of the grid. An intensity scorer determines, for each of a plurality of test grid elements of the plurality of grid elements, a set of intensity scores. Each member of the set is based, at least in part, on intensities of pixels of one or more image features within the test grid element in one of the initial or additional positions. A combined-rank-score generator combines, for each of the initial and additional grid positions, members of sets of rank scores corresponding to the grid position in order to generate a combined rank score for the grid position. A grid alignment adjuster adjusts the alignment of the grid based on a comparison among the combined rank scores.