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Steps in the Modeling Process

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Related Experiment Video

Updated: Jun 27, 2026

Scaled Anatomical Model Creation of Biomedical Tomographic Imaging Data and Associated Labels for Subsequent Sub-surface Laser Engraving SSLE of Glass Crystals

Scaled Anatomical Model Creation of Biomedical Tomographic Imaging Data and Associated Labels for Subsequent Sub-surface Laser Engraving SSLE of Glass Crystals

Published on: April 25, 2017

SlicerMorph photogrammetry: an open-source photogrammetry workflow for reconstructing 3D models.

Oshane O Thomas¹, Chi Zhang², A Murat Maga^1,3

¹Center for Development Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington, 98101, United States of America.

|August 6, 2025

Summary

This summary is machine-generated.

This study introduces an open-source 3D Slicer pipeline for creating accurate skeletal models. The new method improves 3D model reconstruction accuracy for ecological and evolutionary research.

Keywords:

3D morphometrics OpenDroneMap Photogrammetry

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Area of Science:

Paleontology
Computational Biology
3D Imaging

Background:

High-fidelity three-dimensional (3D) models of skeletal specimens are crucial for ecological and evolutionary research.
Existing workflows for 3D model reconstruction can be complex and time-consuming.

Purpose of the Study:

To present a fully open-source pipeline within the 3D Slicer platform for generating accurate 3D skeletal models.
To improve the accuracy and efficiency of 3D model reconstruction for scientific analyses.

Main Methods:

Developed a 3D Slicer extension integrating automatic image masking using the Segment Anything Model (SAM) and surface reconstruction via the OpenDroneMap (NodeODM) engine.
Photographed 14 mountain-beaver skulls and reconstructed 3D models using the new pipeline and a previous workflow.
Compared the accuracy of the reconstructed models against micro-CT references using mean surface distance, root mean square error (RMSE), Hausdorff, and Chamfer metrics.

Main Results:

The improved pipeline, incorporating SAM masking, reduced mean surface distance and RMSE by 10-15% compared to the previous workflow.
Visible artifacts around delicate skeletal elements, such as zygomatic arches, were reduced.
Hausdorff distance showed minimal change, indicating global improvements rather than outlier reduction.

Conclusions:

The new open-source pipeline offers a user-friendly and accurate method for 3D skeletal model reconstruction.
This integrated workflow enhances the quality of 3D models for ecological and evolutionary studies.
The pipeline streamlines the process of masking, scaling, and reconstruction within a single interface.