Robustness of GoIFISHGoIFISH performance with user input. (A) Inter-user variation in background intensity selection from three observers (two trained) when compared to the Gold Standard. (B) Heatmap of coefficient of variation of background intensity in all sample images. Larger shape indicates a higher mean. (C) Inter-user variation in area of segmented cells (nuclear and membrane) and (D) corresponding intensity of HER2 membranes and ER. (E) Permutation testing of accuracy of classifier using either only morphological information or morphological and intensity information for myopepithelial-luminal discrimination (left) and lymphocyte-stromal-tumor discrimination (right).