Disclosed herein is s computer-based method for obtaining and analyzing multi-die scan data of a patterned wafer. The method includes sequentially implementing an operation of scanning a respective plurality of sets of slices on a wafer, and, per each slice segment in a multiplicity of slice segments in the plurality of sets of slices, an operation of performing die-to-multi-die (D2MD) analysis of scan data of the slice segment in order to detect defects in the slice segment. Each set of slices may constitute a subset of the totality of slices on the respective die-column. Sets scanned in a same implementation are analogous to one another, thereby facilitating—in the die-to-multi-die analysis of scan data of a slice segment—taking into account, as reference, scan data of areas on other die-columns, which were scanned in the same implementation.