1. A method for aligning an ordered stack of images from a specimen, comprising the successive steps of: determining (S 40 ), for at least two already aligned images (r i , r, i+1 ) of the ordered stack, the respective misalignments (s i , s i+1 ) with an unaligned image (c i+2 ) which is to be aligned next in the ordered stack; from the at least two aligned images (r i , r i+1 ), selecting (S 50 , S 70 , S 74 , S 76 ) as a reference image (r ref ) that aligned image with which the unaligned image (c i+2 ) has the smallest amount of misalignment (f(s i ), f(s i+1 )); and aligning (S 80 ) the unaligned image (c 1+2 ) with the selected reference image (r ref ).