The Natural Historian’s Guide to the CT Galaxy: Step-by-Step Instructions for Preparing and Analyzing Computed Tomographic (CT) Data Using Cross-Platform, Open Access Software

Authors

T. J. Buser, Oregon State UniversityFollow
O. F. Boyd, Oregon State University
A. Cortés, Oregon State University
Cassandra M. Donatelli, Chapman UniversityFollow
M. A. Kolmann, George Washington University
J. L. Luparell, Oregon State University
J. A. Pfeiffenberger, Temple University
B. L. Sidlauskas, Oregon State University
A. P. Summers, University of Washington

Document Type

Article

Publication Date

4-10-2020

Abstract

The decreasing cost of acquiring computed tomographic (CT) data has fueled a global effort to digitize the anatomy of museum specimens. This effort has produced a wealth of open access digital three-dimensional (3D) models of anatomy available to anyone with access to the Internet. The potential applications of these data are broad, ranging from 3D printing for purely educational purposes to the development of highly advanced biomechanical models of anatomical structures. However, while virtually anyone can access these digital data, relatively few have the training to easily derive a desirable product (e.g., a 3D visualization of an anatomical structure) from them. Here, we present a workflow based on free, open source, cross-platform software for processing CT data. We provide step-by-step instructions that start with acquiring CT data from a new reconstruction or an open access repository, and progress through visualizing, measuring, landmarking, and constructing digital 3D models of anatomical structures. We also include instructions for digital dissection, data reduction, and exporting data for use in downstream applications such as 3D printing. Finally, we provide Supplementary Videos and workflows that demonstrate how the workflow facilitates five specific applications: measuring functional traits associated with feeding, digitally isolating anatomical structures, isolating regions of interest using semi-automated segmentation, collecting data with simple visual tools, and reducing file size and converting file type of a 3D model.

Comments

This article was originally published in Integrative Organismal Biology, volume 2, issue 1, in 2020. https://doi.org/10.1093/iob/obaa009

Recommended Citation

Buser, T.J., Boyd, O.F., Cortés, A., Donatelli, C.M., Kolmann, M.A., Luparell, J.L., Pfeiffenberger, J., Sidlauskas, B.L., Summers, A.P., 2020, The natural historian’s guide to the CT galaxy: step-by-step instructions for preparing and analyzing computed tomographic (CT) data using cross-platform, open access software. Integrative Organismal Biology, 2:1, obaa009. https://doi.org/10.1093/iob/obaa009

Copyright

The authors

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 License.