Automated density-based counting of FISH amplification signals for HER2 status assessment

Background: Automated image analysis can make quantification of FISH signals in histological sections more efficient and reproducible. Current detection-based methods, however, often fail to accurately quantify densely clustered FISH signals. Methods: We propose a novel density-based approach to quantifying FISH signals. Instead of detecting individual signals, this approach quantifies FISH signals in terms of the integral over a density map predicted by Deep Learning. We apply the density-based approach to the task of counting and determining ratios of ERBB2 and CEN17 signals and compare it to common detection-based and area-based approaches. Results: The ratios determined by our approach were strongly correlated with results obtained by manual annotation of individual FISH signals (Pearson's r = 0.907). In addition, they were highly consistent with cutoff-scores determined by a pathologist (balanced concordance = 0.971). The density-based approach generally outperformed the other approaches. Its superiority was particularly evident in the presence of dense signal clusters. Conclusions: The presented approach enables accurate and efficient automated quantification of FISH signals. Since signals in clusters can hardly be detected individually even by human observers, the density-based quantification performs better than detection-based approaches.