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

Publication ,  Journal Article
Rolfe, S; Pieper, S; Porto, A; Diamond, K; Winchester, J; Shan, S; Kirveslahti, H; Boyer, D; Summers, A; Maga, AM
Published in: Methods in Ecology and Evolution
October 1, 2021

Large-scale digitization projects such as #ScanAllFishes and oVert are generating high-resolution microCT scans of vertebrates by the thousands. Data from these projects are shared with the community using aggregate 3D specimen repositories like MorphoSource through various open licenses. We anticipate an explosion of quantitative research in organismal biology with the convergence of available data and the methodologies to analyse them. Though the data are available, the road from a series of images to analysis is fraught with challenges for most biologists. It involves tedious tasks of data format conversions, preserving spatial scale of the data accurately, 3D visualization and segmentations, and acquiring measurements and annotations. When scientists use commercial software with proprietary formats, a roadblock for data exchange, collaboration and reproducibility is erected that hurts the efforts of the scientific community to broaden participation in research. We developed SlicerMorph as an extension of 3D Slicer, a biomedical visualization and analysis ecosystem with extensive visualization and segmentation capabilities built on proven python-scriptable open-source libraries such as Visualization Toolkit and Insight Toolkit. In addition to the core functionalities of Slicer, SlicerMorph provides users with modules to conveniently retrieve open-access 3D models or import users own 3D volumes, to annotate 3D curve and patch-based landmarks, generate landmark templates, conduct geometric morphometric analyses of 3D organismal form using both landmark-driven and landmark-free approaches, and create 3D animations from their results. We highlight how these individual modules can be tied together to establish complete workflow(s) from image sequence to morphospace. Our software development efforts were supplemented with short courses and workshops that cover the fundamentals of 3D imaging and morphometric analyses as it applies to study of organismal form and shape in evolutionary biology. Our goal is to establish a community of organismal biologists centred around Slicer and SlicerMorph to facilitate easy exchange of data and results and collaborations using 3D specimens. Our proposition to our colleagues is that using a common open platform supported by a large user and developer community ensures the longevity and sustainability of the tools beyond the initial development effort.

Duke Scholars

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Published In

Methods in Ecology and Evolution

DOI

EISSN

2041-210X

Publication Date

October 1, 2021

Volume

12

Issue

10

Start / End Page

1816 / 1825

Related Subject Headings

  • 4104 Environmental management
  • 3109 Zoology
  • 3103 Ecology
  • 0603 Evolutionary Biology
  • 0602 Ecology
  • 0502 Environmental Science and Management
 

Citation

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MLA
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Rolfe, S., Pieper, S., Porto, A., Diamond, K., Winchester, J., Shan, S., … Maga, A. M. (2021). SlicerMorph: An open and extensible platform to retrieve, visualize and analyse 3D morphology. Methods in Ecology and Evolution, 12(10), 1816–1825. https://doi.org/10.1111/2041-210X.13669
Rolfe, S., S. Pieper, A. Porto, K. Diamond, J. Winchester, S. Shan, H. Kirveslahti, D. Boyer, A. Summers, and A. M. Maga. “SlicerMorph: An open and extensible platform to retrieve, visualize and analyse 3D morphology.” Methods in Ecology and Evolution 12, no. 10 (October 1, 2021): 1816–25. https://doi.org/10.1111/2041-210X.13669.
Rolfe S, Pieper S, Porto A, Diamond K, Winchester J, Shan S, et al. SlicerMorph: An open and extensible platform to retrieve, visualize and analyse 3D morphology. Methods in Ecology and Evolution. 2021 Oct 1;12(10):1816–25.
Rolfe, S., et al. “SlicerMorph: An open and extensible platform to retrieve, visualize and analyse 3D morphology.” Methods in Ecology and Evolution, vol. 12, no. 10, Oct. 2021, pp. 1816–25. Scopus, doi:10.1111/2041-210X.13669.
Rolfe S, Pieper S, Porto A, Diamond K, Winchester J, Shan S, Kirveslahti H, Boyer D, Summers A, Maga AM. SlicerMorph: An open and extensible platform to retrieve, visualize and analyse 3D morphology. Methods in Ecology and Evolution. 2021 Oct 1;12(10):1816–1825.
Journal cover image

Published In

Methods in Ecology and Evolution

DOI

EISSN

2041-210X

Publication Date

October 1, 2021

Volume

12

Issue

10

Start / End Page

1816 / 1825

Related Subject Headings

  • 4104 Environmental management
  • 3109 Zoology
  • 3103 Ecology
  • 0603 Evolutionary Biology
  • 0602 Ecology
  • 0502 Environmental Science and Management