In the field of cytogenetics, chromosome image analysis or karyotyping from metaphase images plays an imperative role in the diagnosis, prognosis and treatment assessment of different genetic disorders and cancers. This paper is a comprehensive review on different traditional and deep‐based techniques, which are utilized in the design of automated karyotyping systems (AKSs). By this review, a detailed methodology is suggested for the design of end‐to‐end automated karyotyping system (EEAKS) which portrays a sequential multi stage approach. Methods related to all the stages in EEAKS are systematically surveyed by exploring the state of the art literature. Datasets and performance measures incorporated in the past studies are explored. Even though numerous methods were proposed throughout the past three decades, a completely automated framework has not yet been acknowledged. Inferences from this study show that, while various traditional image processing strategies are utilized for pre‐processing and segmentation, machine learning techniques are used only for the classification purpose. In conventional classifiers, artificial neural networks are generally utilized even when the peak performance is given by support vector machines. However, owing to the recent prodigious breakthrough in computer vision, deep neural networks are progressively utilized for developing automated systems. It is seen that deep neural networks are not yet explored in the realm of pre‐processing stage of EEAKS. However, limited number of methods based on convolutional neural networks (CNN) are utilized in all other stages. This review recommends a hybrid CNN for the design of EEAKS, in which all the stages can be automated by sub CNNs. Methodology for generating sufficient datasets is also discussed here which is, indeed, required for further research in this area. This paper concludes with future research directions for the development of a fully automated end‐to‐end karyotyping system.

Segmentation plays an essential role in the design of the automated karyotyping system (AKS). It is pivotal to segment interphase cells and other debris usually found in the input G metaphase images. The performance of AKSs is considerably less when interphase cells and debris are present in the input images. In this article, two semantic segmentation models are proposed. For this experiment, an annotated dataset is generated from the G banded metaphase images which are prepared at Regional Cancer Centre (RCC), Thiruvananthapuram, Kerala, India. Inspired by the results of UNet, a lighter version L‐UNet is developed and experimented with. It shows the validation IoU (Intersection over Union) of 0.9809 and F1‐score of 0.9903 on the RCC dataset and the test IoU of 0.9720 and F1‐score of 0.9858 on the CRCN‐NE dataset. As backbone semantic segmentation models are state of the art, an efficient model, Eff‐UNet, is also proposed here. In this model, EfficientNetB03 acts as the backbone that extracts powerful features and UNet acts as the decoder that predicts the segmentation map. It performs with the validation IoU of 0.9842 and F1‐score of 0.9920 on the RCC dataset and the test IoU of 0.7545 and F1‐score of 0.7778 on the CRCN‐NE dataset. To derive this model, 25 encoder–decoder architectures are evaluated with various top‐performing CNNs (convolutional neural networks) as encoders and segmentation networks as decoders. Results are further compared with various segmentation models and the best results are obtained from the proposed model.