Human induced pluripotent stem cell formation and morphology prediction during reprogramming with time-lapse bright-field microscopy images using deep learning methods

•Deep learning methods detect cells forming human iPS cell in early reprogramming stage.•CNN classifies a brightfield microscopy image as probability images of cell classes with specific features.•U-net segments cells on a microscopy image and classifies to count the cells by its probability images for the early detection.•RNN by training the probability images predicts morphology of future human iPS cell colonies.•Test for 150 sets of time-lapse images from reprogramming CD34+ cells achieved high detection accuracy.