Journal of Zhejiang University

Bio-Design and Manufacturing 2026 Vol.9 No.5 P.914 - 930

High-throughput automated manipulation and imaging analysis of zebrafish larvae

Author(s): Yangning Li,Shang Wu,Xuanyu Zhang,Haina Ji,Yi Wang,Yuan Sun,Lu Zhao,Yong He
Affiliation(s): 1. State Key Laboratory of Fluid Power and Mechatronic Systems & Liangzhu Laboratory, School of Mechanical Engineering, Zhejiang University, Hangzhou 310027, China more
Corresponding email(s): yuansun@zju.edu.cn, lzhao@zju.edu.cn, yongqin@zju.edu.cn
Key Words: Zebrafish, Automation, Machine vision, 3D reconstruction, Melanin

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Yangning Li, Shang Wu, Xuanyu Zhang, Haina Ji, Yi Wang, Yuan Sun, Lu Zhao, Yong He. High-throughput automated manipulation and imaging analysis of zebrafish larvae[J]. Journal of Zhejiang University Science D, 2026, 9(5): 914 - 930.

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author="Yangning Li, Shang Wu, Xuanyu Zhang, Haina Ji, Yi Wang, Yuan Sun, Lu Zhao, Yong He",
journal="Journal of Zhejiang University Science D",
volume="9",
number="5",
pages="914 - 930",
year="2026",
publisher="Zhejiang University Press & Springer",
doi="10.1631/bdm.2500474"
}

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%A Shang Wu
%A Xuanyu Zhang
%A Haina Ji
%A Yi Wang
%A Yuan Sun
%A Lu Zhao
%A Yong He
%J Journal of Zhejiang University SCIENCE D
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%I Zhejiang University Press & Springer
%DOI 10.1631/bdm.2500474

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A1 - Yuan Sun
A1 - Lu Zhao
A1 - Yong He
J0 - Journal of Zhejiang University Science D
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%@ 1869-1951
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Abstract
Chinese Summary
Academic Network
Reviewer Comment

Abstract: Zebrafish (Danio rerio) larvae are optically transparent, small vertebrates that serve as an ideal model for in vivo high-throughput screening. However, automated high-throughput manipulation, imaging, and analysis of live zebrafish larvae remain considerable challenges. Moreover, it is critical to avoid damage to these delicate organisms because even minor injury can impair normal physiological function. To address these challenges, we developed a high-throughput manipulation platform that enables the loading of zebrafish larvae into glass tubes, enabling accurate localization and controlled rotation at a throughput of one fish every 15 s. The platform uses hydrodynamic methods, including a siphon-based system, as the primary driving mechanism to enable adaptive loading and unloading of zebrafish larvae while substantially reducing fluid pressure and minimizing potential flow-induced damage. In addition, the platform integrates machine vision to support automated control and data acquisition throughout the entire workflow. We developed a comprehensive suite of algorithms for automated image segmentation of zebrafish larval videos and three-dimensional (3D) reconstruction of their transparent structures and internal organs. Two distinct 3D reconstruction algorithm pipelines were designed: one is a computationally efficient, lightweight approach optimized for execution on conventional personal computers; the other is a high-speed rendering-based algorithm that requires large-memory computational resources to achieve reconstructions at the original image resolution. Notably, both approaches operate without requiring any additional user-defined parameter tuning. Finally, we demonstrate the platform’s capability by evaluating drug-induced inhibition of zebrafish melanogenesis. This automated platform expands the utility of zebrafish as a versatile, high-throughput model system, facilitating research across diverse fields, including developmental biology, disease modeling, and pharmaceutical and toxicological evaluation.

斑马鱼幼虫高通量自动化操控与成像分析

斑马鱼（Danio rerio）幼虫作为光学透明的小型脊椎动物，是进行活体高通量筛选的理想模式动物，但实现对活体斑马鱼幼虫的高通量自动化操控、成像与分析仍存在诸多挑战。斑马鱼幼虫柔软且脆弱，即便是轻微伤害也可能影响其正常生理功能，在对其进行高通量自动化操控时必须避免对脆弱的斑马鱼幼虫造成损伤。为应对这些挑战，我们开发了一种高通量操控平台，能够将斑马鱼幼体加载至玻璃管中，并实现其精确空间定位与姿态旋转调整，处理通量可达 15 s/尾。该平台以基于虹吸原理的流体动力学方法作为主要驱动机制，实现斑马鱼幼虫的自适应加载与卸载。该方案大幅降低了流体压力，极大程度上减少了流体可能给斑马鱼幼虫带来的损伤。此外，平台集成机器视觉方法实现了全流程的自动化控制和数据采集。我们开发了一套完整的算法，用于斑马鱼幼虫录像的自动化图像分割及其透明结构与内部器官的三维重建。最后，我们通过评估黑色素合成抑制剂对斑马鱼黑色素生成的抑制效应，验证了该平台的功能。这一自动化平台拓展了斑马鱼幼虫作为多功能高通量模型系统的应用潜力，将推动发育生物学、疾病建模、药物与毒理学评估等广泛领域的研究。
关键词：斑马鱼；自动化；机器视觉；三维重建；黑色素