BRCA2 and type 1 diabetes mellitus: Figure 3A shows that Dice-XMBD outperformed all the other methods, followed by Ilastik. Moreover, the performance of cells prediction from Dice-XMBD was the best and the most stable for all three datasets, while Ilastik and Mesmer tended to under-predict cells. CellProfiler predicted less cells in BRCA2 and over-predicted cells in two T1D datasets, as shown in Figures 3B,C. Furthermore, Dice-XMBD predictions contained most of the cells with IOU value higher than 0.8 (Figure 3D and Supplementary Figure 3).