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An Open-Source Photogrammetry Workflow for Reconstructing 3D Models.

C Zhang1, A M Maga1,2

  • 1Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA.

Integrative Organismal Biology (Oxford, England)
|July 19, 2023
PubMed
Summary
This summary is machine-generated.

This study presents an affordable 3D modeling pipeline using OpenDroneMap (ODM) for biological research. While ODM provides accurate 3D models for gross analysis, subtle differences may impact detailed morphometric studies.

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Area of Science:

  • Biological Sciences
  • Computational Biology
  • Morphology

Background:

  • Accurate and economical 3D biological models are crucial for organismal biology research.
  • Structure-from-motion (SFM) photogrammetry offers a flexible and low-cost approach to 3D modeling.
  • Reliance on expensive commercial software and insufficient accuracy assessments hinder photogrammetry adoption in biology.

Purpose of the Study:

  • To present an affordable, open-source SFM photogrammetry pipeline using OpenDroneMap (ODM) and WebODM.
  • To evaluate the geometric accuracy of ODM-derived 3D models by comparing them to microCT scans.
  • To provide guidance for researchers on utilizing this pipeline for 3D biological model generation.

Main Methods:

  • Developed and implemented an SFM photogrammetry pipeline utilizing the open-source OpenDroneMap (ODM) software.
  • Acquired 3D models of 15 *Aplodontia rufa* (mountain beaver) skulls using the ODM pipeline.
  • Assessed geometric accuracy by comparing ODM-derived models against microCT-scanned models of the same specimens.

Main Results:

  • The ODM pipeline produced 3D models with sufficient geometric accuracy (errors ~2%) for gross metric and morphometric analyses.
  • Consistent patterns of shape variation were captured in both ODM and microCT modalities.
  • Subtle differences between modalities can affect landmark placement and downstream shape analysis, especially with low sample variance.

Conclusions:

  • The ODM pipeline offers a cost-effective and accurate solution for 3D biological modeling for many applications.
  • Researchers should not combine photogrammetric and microCT-derived models for geometric morphometric analysis due to potential inaccuracies.
  • A pilot accuracy test is recommended before using SFM photogrammetry models for detailed morphometric studies.