Embryonic heart morphogenesis (EHM) is a complex and dynamic process where the heart transforms from a single tube into a four-chambered pump. This process is of great biological and clinical interest but is still poorly understood for two main reasons. On the one hand, the existing imaging modalities for investigating EHM suffered from either limited penetration depth or limited spatial resolution. On the other hand, current works typically adopted manual segmentation, which was tedious, subjective, and time consuming considering the complexity of developing heart geometry and the large size of images. In this paper, we propose to utilize confocal microscopy imaging with tissue optical immersion clearing technique to image the heart at different stages of development for EHM study. The imaging method is able to produce high spatial resolution images and achieve large penetration depth at the same time. Furthermore, we propose a novel convex active contour model for automatic image segmentation. The model has the ability to deal with intensity fall-off in depth which is characterized by confocal microscopy images. We acquired the images of embryonic quail hearts from day 6 to day 14 of incubation for EHM study. The experimental results were promising and provided us with an insight view of early heart growth pattern and also paved the road for data-driven heart growth modeling. 1. Introduction The heart is the first functioning organ in the embryo. Although the morphology of the heart changes dramatically during development where it transforms from a single tube into a four-chambered pump, the heart functions without interruption to serve the metabolic needs of the rapidly growing embryo [1]. Embryonic heart morphogenesis (EHM) is critically important for long-time survival, and any defects in the developmental mechanism during embryogenesis may result in congenital cardiac anomalies. In fact, congenital heart disease is relatively frequent which affects from 19 to 75 per 1000 births worldwide and has been an important cause of childhood morbidity and mortality [2]. Understanding EHM in normal and malformed hearts, therefore, has been of considerable clinical and biological interest. Despite a large body of research in the last decades [3–8], EHM is still poorly understood mainly because of the complexity of the growing geometry and extremely small size of the developing heart. Thanks to the rapid development of imaging techniques, 3D reconstruction of embryonic hearts from biomedical images has dramatically improved our ability to visualize EHM.
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