Edward Stanley
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Computed Tomography

Computed Tomography applications for museum collections

High Resolution Computed Tomography (HRCT, also known as X-ray microtomography)  is a nondestructive imaging technique that allows the ultra-high-fidelity reconstruction and visualization of external and internal features of non-living objects. This technique has the potential to revolutionize collections and collections-based research, and has many applications in an ever-growing range of biological systems; although HRCT has traditionally been limited to visualizing denser material (bone, fossil etc.), improved hardware and new contrast-enhancing techniques now allow this technology to visualize many different types of soft-anatomy in exquisite detail. The Blackburn Lab is  exploring the myriad research and educational opportunities of this technology as we visualize and quantify the morphology of living and extinct amphibians and reptiles for both systematic and evolutionary studies. Here are some examples of how our work  is benefiting from CT technology.
Click to watch my talk "The Inside Story: How CT Imaging is Revolutionizing Natural History Museums"

Cordylus namakuiyus Skull by UF Herpetology on Sketchfab

Hemiphractus elioti AMNH124113 by UF Herpetology on Sketchfab

Describing new species

As CT is entirely non-destructive, rare and important specimens can be scanned and then digitally dissected. This is particularly useful when describing new species, as it allows a detailed assessment of internal anatomy of type material without having to damage the specimens in any way. CT data reveals important diagnostic characters that help us describe new species, including girlded lizards from Angola, Cordylus namakuiyus, and several new species of horned tree frogs of the genus Hemiphractus, from Central America. An additional bonus to CT scanning is that the scanned data can be converted into annotated models, which help articulate character states and can be shared with collaborators and other interested parties  around the world. (see the interactive 3D models for examples).   
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Amber fossils

Computed tomography provides a way to look inside fossilized specimens and view structures that simply can't be visualized any other way. Over the past few years my co-authors and I have documented and described several lizards and frogs preserved Burmese amber from the Aptian-Cenomanian boundary (99 million years ago). CT-based analyses allowed us to extract skeletal and soft tissue details that were not visible using light microscopy. These observations helped us better place these the specimens in the tree of life. We were able to  produce  3D printed, enlarged replicas of these CT scans, which will be placed on exhibit at several museums and provide important outreach tools for educators and scientists.


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Soft tissue imaging

Using contrasting agents like Lugol's iodine, we are able to visualize relatively low-density tissues like muscles, blood vessels and nerves in high resolution. This is incredibly useful, as it allows us to study anatomical features in ways that would be impossible with other methods. As the staining process is reversible,  we can use this method to study the soft anatomy of specimens that would be too rare or important for traditional, destructive techniques.

Maximizing the impact of
research collections

Natural history museums serve the scientific community as libraries of biodiversity information, containing hundreds of millions of biological and archaeological specimens. These collections are critical resources for a wide range of scientific disciplines. CT technology has the potential to massively increase the amount of data that can be extracted from any and all museum specimens, but can also greatly increase availability of the specimens themselves, through the creation and online curation of digital surrogates. By making research collections broadly and easily accessible we can maximize their applications  for scientists, educators, and anyone else that is interested in learning more about the world around them.

I am a co-PI on the oVert (open vertebrate) Thematic Collections Network- an initiative that aims to CT-scan ~20,000 fluid-preserved vertebrate specimens, representing over 80% of the approximately 10,500 extant genera. Click the Morphosource button below to start exploring this ever-growing, free repository of three-dimensional anatomical data produced by this project
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CT Scanning at the
University of Florida

The Nanoscale research Facility at the University  houses a  Vtome|x M CT scanner from GE. This versatile dual tube system is capable of scanning dense fossil material or scanning low-density specimens at sub-micron resolution. We have recently acquired a new Xradia Versa 620 X-ray CT microscopy system, which is capable of producing scans with voxel resolutions under 500nm.

Post-processing of the CT data is performed using VGStudioMax, a powerful voxel-analysis software package from Volume Graphics.
Book time on the NRF scanner
Check availability of 3D lab Workstations
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  • Home
  • Research Interests
    • CT scanning >
      • CT processing
    • Girdled lizards
  • About Me
  • Contact and links