By imaging HER2 and ER transcripts in 49 archival breast cancer samples with HER2 and ER status previously established by IHC and DNA FISH, and by applying a simple and computationally efficient approach to segment the images in a regular grid of pseudo-cells, we demonstrate that FFPE-smFISH is able to accurately classify tumors belonging to different molecular subtypes, and has an excellent diagnostic performance (best AUC = 0.92 and 0.95 for HER2 and 0.86 and 0.90 for ER using pseudo-cells and manually segmented cells, respectively). Here, ESR1 is linked to breast cancer.