In this study, we present a soft label fully convolutional network (SL-FCN) for automatic segmentation of human epidermal growth factor receptor 2 (HER2) amplification in fluorescence in situ hybridization (FISH) and dual in situ hybridization (DISH) images of invasive breast cancer and papillary thyroid carcinoma (PTC) on Papanicolaou-stained FNA and thin prep (TP) whole slide images (WSIs). Here, ERBB2 is linked to differentiated thyroid carcinoma.