Prion disease is a neurodegenerative pathology characterized by deposits of the aberrant isoform of the prion protein known as scrapie prion protein (PrPsc) in the CNS. The PrPsc aggregates are highlighted by the immunohistochemical (IHC) staining with 12F10 antibody, and they constitute an essential feature to diagnose the disease. The development of specific scanners to digitalize slides recently made it possible to start a technological revolution in pathology since whole slide images (WSIs) can be analyzed with artificial intelligence. In this work, it was developed a pipeline to perform the diagnosis of prion disease from WSIs referring to tissue samples extracted from the cerebellar or the occipital cortex.