The Human Epidermal Growth Factor Receptor 2 (HER2) is a central biomarker in invasive breast cancer, and the HER2 status is predictive of the patient’s response to HER2-targeted treatment. According to the guidelines of the American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP), the HER2 status must be determined by protein expression and/or genetic analysis of breast tissue sections using immunohistochemistry (IHC) and/or in situ hybridization (ISH), respectively. The present protocol is a fully automatic single-cell approach for HER2 IHC quantification that follows ASCO/CAP guidelines, designed with this new scoring regime in mind, i.e. HER2-low and HER2-ultra. It is also configurable to national modifications.