FIGURE 4:

iPSC quality categories defined by the culture experts. (A) Typical morphology of each category. Four morphological categories are visually defined by iPSC culture experts. Undifferentiation: Good iPSCs with high stemness and pluripotency. Cells have little cytoplasm and prominent nucleoli. Cracked: Upper-middle quality. Cells still have a morphology similar to that of undifferentiated cells, but some kind of differentiation-related activity appears as cracks. Built-up: Lower-middle quality. Cells are crowded, stacking on top of each other, and cell morphology cannot be observed at all. Differentiation: Low quality. Totally differentiated and not useful for the subsequent differentiation process. Cells of this category have a flat, dark, and large appearance compared with the cells of the other categories. (B) t-SNE plot based on the image features extracted by the VQ-VAE-2 model trained with the A3 data set. Each color represents images of the quality categories defined by the experts, which mostly exist in different regions in the feature space despite this being an unsupervised analysis, which does not involve any training with expert annotations.