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SignificanceAutomated understanding of human embryonic stem cell (hESC) videos is essential for the quantified analysis and classification of various states of hESCs and their health for diverse applications in regenerative medicine.AimThis paper aims to develop an ensemble method and bagging of deep learning classifiers as a model for hESC classification on a video dataset collected using a phase contrast microscope.ApproachThe paper describes a deep learning-based random network (RandNet) with an autoencoded feature extractor for the classification of hESCs into six different classes, namely, (1)cell clusters, (2)debris, (3)unattached cells, (4)attached cells, (5)dynamically blebbing cells, and (6)apoptotically blebbing cells. The approach uses unlabeled data to pre-train the autoencoder network and fine-tunes it using the available annotated data.ResultsThe proposed approach achieves a classification accuracy of 97.23 ± 0.94 % and outperforms the state-of-the-art methods. Additionally, the approach has a very low training cost compared with the other deep-learning-based approaches, and it can be used as a tool for annotating new videos, saving enormous hours of manual labor.ConclusionsRandNet is an efficient and effective method that uses a combination of subnetworks trained using both labeled and unlabeled data to classify hESC images.