A Robust Framework of Chromosome Straightening with ViT-Patch GAN

Chromosomes exhibit non-rigid and non-articulated nature with varying degrees of curvature. Chromosome straightening is an essential step for subsequent karyotype construction, pathological diagnosis and cytogenetic map development. However, robust chromosome straightening remains challenging, due to the unavailability of training images, distorted chromosome details and shapes after straightening, as well as poor generalization capability. We propose a novel architecture, ViT-Patch GAN, consisting of a motion transformation generator and a Vision Transformer-based patch (ViT-Patch) discriminator. The generator learns the motion representation of chromosomes for straightening. With the help of the ViT-Patch discriminator, the straightened chromosomes retain more shape and banding pattern details. The proposed framework is trained on a small dataset and is able to straighten chromosome images with state-of-the-art performance for two large datasets.

A Novel Application of Image-to-Image Translation: Chromosome Straightening Framework by Learning from a Single Image

In medical imaging, chromosome straightening plays a significant role in the pathological study of chromosomes and in the development of cytogenetic maps. Whereas different approaches exist for the straightening task, they are mostly geometric algorithms whose outputs are characterized by jagged edges or fragments with discontinued banding patterns. To address the flaws in the geometric algorithms, we propose a novel framework based on image-to-image translation to learn a pertinent mapping dependence for synthesizing straightened chromosomes with uninterrupted banding patterns and preserved details. In addition, to avoid the pitfall of deficient input chromosomes, we construct an augmented dataset using only one single curved chromosome image for training models. Based on this framework, we apply two popular image-to-image translation architectures, U-shape networks and conditional generative adversarial networks, to assess its efficacy. Experiments on a dataset comprising of 642 real-world chromosomes demonstrate the superiority of our framework as compared to the geometric method in straightening performance by rendering realistic and continued chromosome details. Furthermore, our straightened results improve the chromosome classification, achieving 0.98%-1.39% in mean accuracy.