3DPhenoFish

3DPhenoFish extracts morphological phenotypes from three-dimensional (3D) point cloud data of fish to enable quantitative analysis of two-dimensional and three-dimensional traits.

Key Features:

• Automated Phenotype Extraction: Extracts two-dimensional (2D) and three-dimensional (3D) morphological traits from point cloud data.
• Background Elimination: Performs background elimination to isolate fish point clouds.
• Coordinate Normalization: Applies coordinate normalization to standardize spatial orientation and scale.
• Image Segmentation: Performs image segmentation to delineate anatomical regions.
• Key Point Recognition: Automatically identifies 18 anatomical key points for phenotype calculation.
• Phenotype Calculation: Computes traditional 2D morphological measures and 3D phenotypes such as area and volume.
• Customization and Fine-Tuning: Supports adjustment of key points and custom definitions of phenotypes.
• High Correlation with Manual Measurements: Validation shows a linear correlation greater than 0.94 with manual measurements.
• Species and Population Discrimination: Provides informative traits that discriminate between species and among populations within species.
• High-Throughput Data Handling: Processes large point cloud datasets for high-throughput phenotyping.

Scientific Applications:

• Functional Gene Mapping: Provides precise morphological measurements that support association of phenotypes with genetic markers.
• Artificial Breeding Programs: Supplies detailed phenotypic data to inform selective breeding decisions.
• Population-Based Studies: Enables differentiation of populations for ecological and conservation analyses.
• Aquaculture Research: Delivers quantitative phenotypes relevant to breeding and management in aquaculture.

Methodology:

Captures high-resolution point cloud data and applies integrated algorithms for background elimination, coordinate normalization, image segmentation, key point recognition, and phenotype extraction, as demonstrated on endemic Schizothoracinae species.