1. A method for aligning an ordered stack of images from a specimen, comprising the successive steps of: determining, for at least two already aligned images of the ordered stack, the respective misalignments with an unaligned image which is to be aligned next in the ordered stack; discarding the unaligned image to be aligned next from the ordered stack of images if all of the determined misalignments amounts are above a certain threshold; replacing the discarded image with an interpolated image generated by an interpolation of the aligned images; from the at least two aligned images, selecting as a reference image that aligned image with which the unaligned image has the smallest amount of misalignment; and aligning the unaligned image with the selected reference image; wherein all the above steps are performed via a processor.