Automatic Segmentation and Cardiac Mechanics Analysis of Evolving Zebrafish Using Deep Learning

• Main Authors: Bohan Zhang, Kristofor E. Pas, Toluwani Ijaseun, Hung Cao, Peng Fei, Juhyun Lee
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2021-06-01
• Series: Frontiers in Cardiovascular Medicine
• Subjects: U-net; LSFM; segmentation; zebrafish; cardiac mechanics
• Online Access: https://www.frontiersin.org/articles/10.3389/fcvm.2021.675291/full

Background: In the study of early cardiac development, it is essential to acquire accurate volume changes of the heart chambers. Although advanced imaging techniques, such as light-sheet fluorescent microscopy (LSFM), provide an accurate procedure for analyzing the heart structure, rapid, and robust segmentation is required to reduce laborious time and accurately quantify developmental cardiac mechanics.Methods: The traditional biomedical analysis involving segmentation of the intracardiac volume occurs manually, presenting bottlenecks due to enormous data volume at high axial resolution. Our advanced deep-learning techniques provide a robust method to segment the volume within a few minutes. Our U-net-based segmentation adopted manually segmented intracardiac volume changes as training data and automatically produced the other LSFM zebrafish cardiac motion images.Results: Three cardiac cycles from 2 to 5 days postfertilization (dpf) were successfully segmented by our U-net-based network providing volume changes over time. In addition to understanding each of the two chambers' cardiac function, the ventricle and atrium were separated by 3D erode morphology methods. Therefore, cardiac mechanical properties were measured rapidly and demonstrated incremental volume changes of both chambers separately. Interestingly, stroke volume (SV) remains similar in the atrium while that of the ventricle increases SV gradually.Conclusion: Our U-net-based segmentation provides a delicate method to segment the intricate inner volume of the zebrafish heart during development, thus providing an accurate, robust, and efficient algorithm to accelerate cardiac research by bypassing the labor-intensive task as well as improving the consistency in the results.