Towards Precision Cardiovascular Analysis in Zebrafish: The ZACAF Paradigm

• Published in: arXiv.org 2024-02
• Main Authors: Amir Mohammad Naderi, Casey, Jennifer G, Mao-Hsiang, Huang, Victorio, Rachelle, Chiang, David Y, MacRae, Calum, Cao, Hung, Gupta, Vandana A
• Format: Article
• Language: English
• Subjects: Data augmentation; Datasets; Deep learning; Image processing; Performance enhancement; Testing time; Zebrafish
• ISSN: 2331-8422

Quantifying cardiovascular parameters like ejection fraction in zebrafish as a host of biological investigations has been extensively studied. Since current manual monitoring techniques are time-consuming and fallible, several image processing frameworks have been proposed to automate the process. Most of these works rely on supervised deep-learning architectures. However, supervised methods tend to be overfitted on their training dataset. This means that applying the same framework to new data with different imaging setups and mutant types can severely decrease performance. We have developed a Zebrafish Automatic Cardiovascular Assessment Framework (ZACAF) to quantify the cardiac function in zebrafish. In this work, we further applied data augmentation, Transfer Learning (TL), and Test Time Augmentation (TTA) to ZACAF to improve the performance for the quantification of cardiovascular function quantification in zebrafish. This strategy can be integrated with the available frameworks to aid other researchers. We demonstrate that using TL, even with a constrained dataset, the model can be refined to accommodate a novel microscope setup, encompassing diverse mutant types and accommodating various video recording protocols. Additionally, as users engage in successive rounds of TL, the model is anticipated to undergo substantial enhancements in both generalizability and accuracy. Finally, we applied this approach to assess the cardiovascular function in nrap mutant zebrafish, a model of cardiomyopathy.