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SlicerMorph: An open and extensible platform to retrieve, visualize and analyze 3D morphology.

Sara Rolfe^1,2, Steve Pieper³, Arthur Porto^4,5

¹University of Washington, Friday Harbor Marine Laboratories, San Juan, WA.

Methods in Ecology and Evolution

|May 22, 2025

Summary

SlicerMorph is a new open-source software extension that simplifies the analysis of 3D vertebrate scans. It enables biologists to easily conduct quantitative research on organismal form and shape, fostering collaboration and data sharing.

Keywords:

3D visualization Statistical shape analysis morphometrics quantitative morphology

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Area of Science:

Evolutionary Biology
Computational Biology
Bioinformatics

Background:

Large-scale digitization projects (#ScanAllFishes, oVert) are producing vast amounts of 3D microCT scan data for vertebrates.
Existing data repositories (e.g., MorphoSource) facilitate open access to these 3D specimens.
Analyzing this data presents challenges for biologists, including data conversion, 3D visualization, segmentation, and measurement acquisition.

Purpose of the Study:

To develop an accessible, open-source software tool to streamline the analysis of 3D vertebrate scans.
To facilitate quantitative research in organismal biology by simplifying the workflow from raw image data to morphometric analysis.
To foster a collaborative community of biologists utilizing 3D specimen data.

Main Methods:

Developed SlicerMorph, an extension for 3D Slicer, a biomedical visualization and analysis platform.
Integrated modules for retrieving open-access 3D models, annotating landmarks (curve and patch-based), and generating templates.
Incorporated functionalities for geometric morphometric analyses (landmark-driven and landmark-free) and creating 3D animations.
Provided supplementary training through short courses and workshops on 3D imaging and morphometrics.

Main Results:

SlicerMorph offers a comprehensive workflow for analyzing 3D organismal form, from image sequences to morphospace.
The software addresses challenges in data format conversion, spatial scale preservation, and annotation.
Enabled users to perform advanced morphometric analyses and visualize results effectively.

Conclusions:

SlicerMorph empowers organismal biologists to conduct quantitative research using 3D specimens more efficiently.
The open-source nature and community support aim to ensure the long-term sustainability and accessibility of the tool.
Promotes data exchange, collaboration, and broader participation in 3D-based biological research.