Abstract: A method for genotype classification including the steps of acquiring a pair of scanned images of an SNP sample for a plurality of individuals selected from a population, wherein one image of the image pairs is associated with a first allele and the other image of the image pair is associated with a second allele of the sample. For both images of the associated scanned image pair of each sample: performing pre-processing of the image to remove scanning noises from the image, obtaining total sample intensity information from the image, defining a sample boundary to encompass at least a substantial part of the luminous pixels of the image, matching said sample boundary to the image, and performing a pixel-based processing of the image using the matched sample boundary in order to obtain image quality information with respect to said sample.