Micro computed tomography data processing for integrative anatomy
The combination of Thermo Scientific Amira and Avizo Software provides a powerful 3D segmentation and visualization solution. Rapid processing of difficult data sets and a comprehensive set of 3D modeling tools lend it to widespread application in paleontological and biological research.
Dr. Laura Porro explains how Amira-Avizo Software is vital to her research in integrative anatomy.
“I have consistently found Amira-Avizo Software to be the best-suited visualization software for my research needs.”
Computed tomography (CT) is an essential technique in anatomy. It enables non-destructive imaging of biological structures, revealing the density of different tissues. Dr. Laura Porro of University College London has been using Amira-Avizo Software for over a decade to process anatomical CT data of all kinds.
“I use Amira-Avizo Software to process medical imaging data of humans and living animals to obtain information on skeletal shape and create 3D models,” says Dr. Porro. “More recently, my colleagues and I have been using various stains and contrast-enhanced CT scanning along with Amira-Avizo Software to visualize soft tissue anatomy in a range of different species, from fish and frogs to reptiles and birds.”
Using chemical stains in conjunction with micro-computed tomography ("μ" CT) enables “digital dissection” of specimens. Detailed 3D reconstructions of soft- and hard-tissue anatomy can be extracted and analyzed without the need to ever pick up a scalpel. As well as being non-destructive, these techniques permit the visualization of very small and fragile specimens without altering the 3D topology of anatomical structures. Porro’s published research includes digital dissections of two teleost fish, the head of the rock dove (Columba livia), and the African clawed frog (Xenopus laevis).1–3
“Our greatest challenge is posed by segmenting imaging data of fossil animals, which often features poor contrast between fossil bones and surrounding rock,” notes Porro.
“Over the years, Amira-Avizo Software has repeatedly proven to be the best solution for processing these difficult data sets, providing anatomical data that is fundamental for understanding the shape of the tree of life.”
Amira-Avizo Software can be used to process μCT data and create detailed interactive 3D reconstructions for wider distribution to the public, students, and researchers.
“The interpolation, smoothing, and transformation tools available within Amira-Avizo Software are ideal for manipulating elements in 3D space, allowing us to remove millions of years of damage and deformation…”
A suite of 3D image processing tools within Amira-Avizo Software can be used to modify CT data from fossil samples, enabling reconstructive manipulation of 3D models. Porro and her colleagues use these tools to “digitally restore” fossils of extinct species, enabling them to “see for the first time how these remarkable animals appeared in life.” 4,5
Using Amira-Avizo Software, Porro and her team segmented scans of fossil specimens to discern the bone structures of these species in detail.
Segmentation of CT data of the extinct tetrapod Acanthostega gunnari. Ref: Porro LB, Rayfield EJ, Clack JA (2015) Descriptive Anatomy and Three-Dimensional Reconstruction of the Skull of the Early Tetrapod Acanthostega gunnari Jarvik, 1952. PLoS ONE 10(3): e0118882.4
“Tools within Amira-Avizo Software are essential for preparing and exporting models for further applications, including 3D morphometric analyses and biomechanical modeling.”
The 3D models produced using Amira-Avizo Software are not just useful for visualization. Porro and her colleagues used the software to reconstruct the musculoskeletal anatomy of the skull of the extinct marine crocodile Pelagosaurus, comparing it to that of the living Indian gharial Gavialis.
Finite element analysis of the resulting 3D model enabled investigation of stress distribution in the skull, giving insight into the hunting and eating behaviors of Pelagosaurus.6
Comparison of finite element modeling of the mandible of Alligator mississippiensis using 3D models from Amira-Avizo Software showed that this approach closely matches experimental in vivo results.7
In a recent project, Porro used Amira-Avizo Software to repair the skeleton of an extinct animal specimen at UCL’s Grant Museum of Zoology, highlighting the value of simple and accurate 3D modeling for education and collaboration. The specimen in question—the skeleton of a quagga Equus quagga, a relative of the living zebra—was missing its left hind leg. The existing right hind leg was scanned and mirrored to create a 3D model, from which a 3D-printed replacement could be fabricated.8
Amira-Avizo Software provides a complete solution for each step of the workflow, from segmentation of challenging images to 3D rendering to physical modeling.
“Amira-Avizo Software is an absolutely essential tool for carrying out cutting-edge anatomical and biomechanical work within our research group, one I anticipate we will continue using for many years to come.”
By Dr. Laura Porro
Lecturer in Anatomy
Centre for Integrative Anatomy
Department of Cell and Developmental Biology
University College London
Images and text are courtesy of Dr. Laura Porro, University College London.
1. Jones, M.E.H., Button, D.J., Barrett, P.M. et al. Digital dissection of the head of the rock dove (Columba livia) using contrast-enhanced computed tomography. Zoological Lett 5, 17 (2019). https://doi.org/10.1186/s40851-019-0129-z.
2. Brocklehurst R, Porro L, Herrel A, Adriaens D, Rayfield E. A digital dissection of two teleost fishes: comparative functional anatomy of the cranial musculoskeletal system in pike (Esox lucius) and eel (Anguilla anguilla). J Anat. 2019 Aug;235(2):189-204. doi: 10.1111/joa.13007.
3. Porro LB, Richards CT. Digital dissection of the model organism Xenopus laevis using contrast-enhanced computed tomography. J Anat. 2017 Aug;231(2):169-191. doi: 10.1111/joa.12625.
4. Porro LB, Rayfield EJ, Clack JA (2015) Descriptive Anatomy and Three-Dimensional Reconstruction of the Skull of the Early Tetrapod Acanthostega gunnari Jarvik, 1952. PLoS ONE 10(3): e0118882. https://doi.org/10.1371/journal.pone.0118882.
5. Porro LB, Witmer LM, Barrett PM. Digital preparation and osteology of the skull of Lesothosaurus diagnosticus (Ornithischia: Dinosauria). PeerJ. 2015 Dec 21;3:e1494. doi: 10.7717/peerj.1494.
6. Ballell, A., Moon, B.C., Porro, L.B., Benton, M.J. and Rayfield, E.J. (2019), Convergence and functional evolution of longirostry in crocodylomorphs. Palaeontology, 62: 867-887. https://doi.org/10.1111/pala.12432.
7. Porro LB, Metzger KA, Iriarte-Diaz J, Ross CF. In vivo bone strain and finite element modeling of the mandible of Alligator mississippiensis. J Anat. 2013;223(3):195-227. doi:10.1111/joa.12080.
8. Nigel R. Larkin, Laura B. Porro; Three legs good, four legs better: Making a quagga whole again with 3D printing. Collection Forum 1 January 2016; 30 (1-2): 73–84. doi: https://doi.org/10.14351/0831-4985-30.1.73.