Induced pluripotent stem cells (iPSCs), which are created from an adult cell that has been reprogrammed, enable the development of an unlimited source of any type of human cells needed for drug discovery and clinical applications . iPSCs are able to help track the earliest disease-causing events in cells and can be used as sources of various cell-based therapies. Because a healthy quality of undifferentiated iPSCs is an essential requisite for further experimental and therapeutic approaches, the rapid and robust estimation of iPSC quality is very important to meet growing demands [2–4]. The morphological structure of a healthy or good-quality iPSC colony commonly has tightly compacted round cells and an explicit boundary, whereas unhealthy or bad-quality colonies show a different morphology . The present approach of evaluating the quality of iPSCs on the basis of colony morphology is predominantly subjective and can strongly differ according to individual skills. Therefore, a quantitative system for the rapid and accurate segmentation and estimation of colony quality is essential in order to reduce classification errors. Furthermore, removal of the use of fluorescent labeling or other chemical reagents would be helpful in preparing the iPSCs for additional research experiments.