Computer-Assisted Annotation of Digital H&E/SOX10 Dual Stains Generates High-Performing Convolutional Neural Network for Calculating Tumor Burden in H&E-Stained Cutaneous Melanoma

Deep learning for the analysis of H&E stains requires a large annotated training set. This may form a labor-intensive task involving highly skilled pathologists. We aimed to optimize and evaluate computer-assisted annotation based on digital dual stains of the same tissue section. H&E stains of primary and metastatic melanoma (N = 77) were digitized, re-stained with SOX10, and re-scanned. Because images were aligned, annotations of SOX10 image analysis were directly transferred to H&E stains of the training set. Based on 1,221,367 annotated nuclei, a convolutional neural network for calculating tumor burden (CNN(TB)) was developed. For primary melanomas, precision of annotation was 100% (95%CI, 99% to 100%) for tumor cells and 99% (95%CI, 98% to 100%) for normal cells. Due to low or missing tumor-cell SOX10 positivity, precision for normal cells was markedly reduced in lymph-node and organ metastases compared with primary melanomas (p < 0.001). Compared with stereological counts within skin lesions, mean difference in tumor burden was 6% (95%CI, −1% to 13%, p = 0.10) for CNN(TB) and 16% (95%CI, 4% to 28%, p = 0.02) for pathologists. Conclusively, the technique produced a large annotated H&E training set with high quality within a reasonable timeframe for primary melanomas and subcutaneous metastases. For these lesion types, the training set generated a high-performing CNN(TB), which was superior to the routine assessments of pathologists.