Understanding embryonic heart morphogenesis through automatic segmentation and confocal imaging with optical clearing

Embryonic heart morphogenesis (EHM) is a developmental process where the heart transforms from a single tube into a four-chambered pump. It is of great biological and clinical interest, but is still poorly understood for two main reasons. On 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 clearing technique to image the heart at different stages of development for EHM study. This imaging method is able to produce high spatial resolution images and achieve high penetration depth. Furthermore, we propose a novel convex active contour model for automatic image segmentation. The model has the ability of dealing with intensity fall-off the depth which is characterized by confocal microscopy images. We scan and segment embryonic quail hearts from day 6 to day 14 of incubation. The experimental results show the efficiency of the proposed segmentation method and the usefulness of this imaging data, and provide us an insight view of early heart development.