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3DPhenoFish: Application for two- and three-dimensional fish morphological phenotype extraction from point cloud

Yu-Hang Liao¹, Chao-Wei Zhou^2,3, Wei-Zhen Liu¹

¹Department of Computer Science, Wuhan University of Technology, Wuhan, Hubei 430070, China.

Zoological Research

|July 8, 2021

Summary

3DPhenoFish software automates fish morphological phenotyping from 3D data, offering an efficient and accurate alternative to manual measurements. This tool aids in aquaculture, functional gene mapping, and conservation studies by providing detailed fish morphology insights.

Keywords:

3D scanning Fish Morphology Phenomics Point cloud

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Area of Science:

Aquaculture and Ecology
Bioinformatics
Ichthyology

Background:

Traditional fish phenotyping is time-consuming, labor-intensive, and subjective.
Accurate morphological data is crucial for artificial breeding, gene mapping, and ecological studies.
Existing methods lack efficiency and objectivity in capturing complex fish phenotypes.

Purpose of the Study:

To develop an automated software tool, 3DPhenoFish, for extracting fish morphological phenotypes from 3D point cloud data.
To provide an efficient, accurate, and customizable solution for high-throughput fish phenotyping.
To overcome the limitations of traditional manual phenotyping methods.

Main Methods:

Development of algorithms for background elimination, coordinate normalization, image segmentation, key point recognition, and phenotype extraction.
Integration of these algorithms into an intuitive user interface for automated 2D and 3D phenotype extraction.
Application of 3DPhenoFish for high-throughput phenotyping of four Schizothoracinae fish species.

Main Results:

3DPhenoFish accurately extracts 18 key points, 2D traits, and 3D phenotypes (area, volume) from 3D point cloud data.
Phenotypic data from 3DPhenoFish showed a high linear correlation (>0.94) with manual measurements.
The software successfully discriminated between different species and populations of Schizothoracinae fish.

Conclusions:

3DPhenoFish is an efficient, accurate, and customizable open-source tool for automated fish morphological phenotyping.
The software addresses challenges associated with manual measurements, enabling advanced research in fish breeding, genetics, and conservation.
3DPhenoFish facilitates high-throughput analysis, supporting diverse applications in aquaculture and ecological research.