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Automatic body morphometric analysis of adult zebrafish using microCT
Mohammed Mushtak Kanani1, Ronald Young Kwon1,2,3
1School of Medicine, University of Washington, Seattle, Washington, United States of America.
Plos One
|August 3, 2026
Summary
This study introduces automated methods using FIJI/ImageJ for calculating morphometric measures from micro-computed tomography (microCT) scans of zebrafish. These new techniques improve data collection efficiency and accuracy for musculoskeletal research.
Area of Science:
- Zebrafish (Danio rerio) as a model organism in genetics, development, disease, regeneration, and evolution.
- Application of micro-computed tomography (microCT) for quantitative 3D morphometric analysis.
- Advancements in automated image analysis for biological research.
Background:
- Zebrafish are crucial models for studying musculoskeletal systems.
- Micro-computed tomography (microCT) enables detailed 3D morphometric analysis in zebrafish.
- Current manual methods for calculating morphometric measures from microCT scans are time-consuming.
Purpose of the Study:
- To develop fully automated methods for calculating key morphometric measures from microCT scans of adult zebrafish.
- To streamline the analysis of lean volume, fineness ratio, swim bladder dimensions, and standard length.
- To provide an accessible tool for researchers using zebrafish models.
Main Methods:
- Utilizing built-in functions within the open-source software FIJI/ImageJ.
- Combining functions to create automated ImageJ macros for morphometric analysis.
- Validating automated methods against manual and semi-automated approaches.
Main Results:
- Automated methods accurately compute morphometric measures comparable to manual techniques.
- Significant improvement in data collection throughput.
- Elimination of inter-observer variability in measurements.
- Successful implementation as accessible ImageJ macros.
Conclusions:
- Fully automated methods for zebrafish morphometrics using microCT are feasible and effective.
- FIJI/ImageJ macros offer an efficient and reproducible solution for researchers.
- This advancement facilitates broader use of microCT in zebrafish research.
