Employing 2-plex and 3-plex chromogenic IHC protocols, we applied the workflow to a cohort of 81 HER2+ breast cancer patients and solved the following technical challenges: 1) computer-assisted, automatic transfer of the tumor mask outlines between slides, 2) generation of an analysis pipeline to quantify distinct immune cell types inside the tumor, on the tumor border and outside of the tumor, 3) determination of sources of error in association with the transfer of the tumor mask and affecting the regional quantification of immune cell populations. This evidence concerns the gene ERBB2 and breast cancer.