Evaluating structural changes in a sample resulting from a treatment of the sample. At least one sample of the material is scanned before and after the treatment and a first and a second image of the sample are obtained. The first and the second images are registered in a full spatial resolution using at least one region of the first image and at least one region of the second image, the regions corresponding to the same part of the sample. The registered images are analyzed and the changes in each sample caused by the performed treatment are evaluated.