3DPhenoFish: Application for two- and three-dimensional fish morphological phenotype extraction from point cloud analysis
Yu-Hang Liao, 武汉理工大学计算机科学与技术学院，湖北 武汉 430000，中国, Chaowei Zhou, Weizhen Liu, Jingyi Jin, Dongye Li, Fei Liu, Dingding Fan, Yu Zou, Zen-Bo Mu, Shen Jian, Chunna Liu, Shijun Xiao, Xiaohui Yuan, Haiping Liu, 西藏自治区农牧科学院水产科学研究所，西藏 拉萨 850000，中国, 西南大学水产学院淡水鱼类繁殖与发育重点实验室（教育部），重庆 400000，中国, 嘉兴市经济霉菌学新种质育种重点实验室，浙江 嘉兴 314000，中国, 华电西藏能源有限责任公司，西藏 拉萨 850000，中国, 中国水利水电科学研究院，北京 100000，中国
Abstract
Fish morphological phenotypes are important resources in artificial breeding, functional gene mapping, and population-based studies in aquaculture and ecology. Traditional morphological measurement of phenotypes is rather expensive in terms of time and labor. More importantly, manual measurement is highly dependent on operational experience, which can lead to subjective phenotyping results. Here, we developed 3DPhenoFish software to extract fish morphological phenotypes from three-dimensional (3D) point cloud data. Algorithms for background elimination, coordinate normalization, image segmentation, key point recognition, and phenotype extraction were developed and integrated into an intuitive user interface. Furthermore, 18 key points and traditional 2D morphological traits, along with 3D phenotypes, including area and volume, can be automatically obtained in a visualized manner. Intuitive fine-tuning of key points and customized definitions of phenotypes are also allowed in the software. Using 3DPhenoFish, we performed high-throughput phenotyping for four endemic Schizothoracinae species, including <i>Schizopygopsis younghusbandi</i>, <i>Oxygymnocypris stewartii</i>, <i>Ptychobarbus dipogon</i>, and <i>Schizothorax oconnori</i>. Results indicated that the morphological phenotypes from 3DPhenoFish exhibited high linear correlation (>0.94) with manual measurements and offered informative traits to discriminate samples of different species and even for different populations of the same species. In summary, we developed an efficient, accurate, and customizable tool, 3DPhenoFish, to extract morphological phenotypes from point cloud data, which should help overcome traditional challenges in manual measurements. 3DPhenoFish can be used for research on morphological phenotypes in fish, including functional gene mapping, artificial selection, and conservation studies. 3DPhenoFish is an open-source software and can be downloaded for free at https://github.com/lyh24k/3DPhenoFish/tree/master.