Extended Data Fig. 2: Visual quality assessment of virtually stained IHC images of the EMPaCT prostate cancer TMA.

(A) Example virtual TMA cores across all six markers (left column) and selected zoomed in regions (middle column) that highlight accurate staining patterns. Real reference IHC images for each marker are given on the right column. We observed that AR+ and NKX3.1+ cells exhibited correct distribution in the luminal epithelial compartment of the prostatic glands and nuclear localization. Furthermore, a few NKX3.1+ cells in stromal regions (possibly stroma-invading tumor cells) were correctly predicted. Similarities in specific, matched areas between virtual and real IHC images were mainly assessed for staining pattern and overall intensity levels: we observed that the expression of markers indicative of tumor-specific molecular profile, such as loss of TP53 and ERG overexpression, did not largely deviate between virtual and real images at a TMA core level, which would be crucial for diagnostic applicability.(B) Same as (A) but highlighting regions with inaccurate or inconclusive staining. We observed non-specific signal in extra-cellular-matrix/stroma regions (NKX3.1, p53, ERG), occasional false nuclear expression (CD44), and systematic lack of recognition of CD146+ vascular structures.