SI Bio-Imaging Research (SIBIR) Center

Former NMNH postdoctoral fellow Maya Yamato and NMNH curator of fossil marine mammals Nick Pyenson used our CT scanner to trace the development of fetal ear bones in 56 specimens from 10 different families of toothed and baleen whales. They observed how ears develop in unborn whales of modern species, and compared these changes with those reflected in the fossilized ears of extinct whales over the course of millions of years. Their findings confirmed that changes in the development of ear bones in the womb paralleled changes observed throughout whale evolution, providing new insight about how whales successfully made the dramatic evolutionary shift from land to sea and adapted to hearing underwater. More information is available in the March 11, 2015 issue of PLOS ONE.

Virtopsy, a term coined by Professor Richard Dirnhofer in 1998, brings the science of autopsy into the digital age. This non-invasive, virtual autopsy defines an interdisciplinary use of sophisticated imaging methods to investigate remains not suited for autopsy or prior to autopsy. External contours can be reproduced or models and internal features can be visualized.

At the National Museum of Natural History (NMNH), virtopsy begins with high quality computerized tomography (CT) scanning that is critical to ultimately achieve detailed results through intricate post processing methods. The scans, taken using a spiral CT, result in transverse, or axial, slices approximately 0.62mm thick. Each slice can be examined individually or stacked with others to reconstitute (reconstruct) the original specimen. When stacked, these thin slices result in 3D models with minimal “stepping” at the junction of each slice.

“Stepping” occurs when the computer is unable to extrapolate enough data to create smooth contours or transitions from one CT slice to the next. With a high number of thin slices, the resulting object has almost invisible steps between the slices. This allows maximum reproducibility of the original object while being able to concentrate on the portion under study. These scans, of course, remain available indefinitely to be reexamined, reproduced, and studied even decades later.

For further analysis at the NMNH, we use a soft tissue protocol long used on living persons that gives a maximum range of gray scale with less high contrast. We import the CT scan series into Mimics software (Materialise, NV, Belgium). This software allows a specific gray-scale (Hounsfield value) range to be identified throughout the object and then tinted a certain color. This process is called segmentation. For example, a gray-scale indicating bone can be identified and colored. When the program finds and colors all areas of similar gray, any bones in the specimen will be revealed. Other gray-scale ranges, tinted other colors, make it possible to distinguish internal organs and skin, including subtle facial features such as wrinkles and eyelid folds. This process clearly reveals inclusions, foreign bodies, and artifacts. Manual segmentation is required in those cases where a lot of mummified tissue is present, as well as clothing, or foreign materials of similar Hounsfield values.

We recently used this combination of thin CT scans and soft tissue gray-scales on mummies of the Basketmaker culture curated at Harvard University’s Peabody Museum of Archaeology and Ethnology and at the University of Pennsylvania Museum of Archaeology and Anthropology. The Harvard mummies were physically examined in 1999 without disturbing wrappings or blankets. At that time, notes were made of visible external features including descriptions of garments and blankets and hair lengths were measured. From detailed observations, a mummy’s gender as well as approximate age, height and preservation were noted. In early 2000, the mummies were x-rayed and scanned by CT. Additional modelling though gray-scale programs waited until 2014.

The scans that made it possible to see beneath obscuring wraps and blankets also made it possible to digitally examine not just the whole skeleton, but individual bones, as well as the ability to assess organ preservation. Bone lengths to determine height, muscle attachment sites to suggest physical activities, joint changes to reveal diseases such as arthritis or cases of osteomyelitis were now measurable or detectable. In addition, crown wear, caries, and abscesses could now be documented in teeth that had not been visible in well-preserved heads. Wear on masticatory surfaces contributed information on diet; dental abscesses and antemortem loss suggested overall health. In some cases virtopsy information on dental development confirmed the original age estimate; in other cases the age was radically revised. While cause of death was not always discernable, a 14-year-old girl clearly died from complications of child birth, something not even considered during initial evaluation.

Gray-scale virtopsy becomes essential when remains are very poorly preserved. In such situations, a CT scan of the clump of soil encasing the object allows the bone to be virtually separated from the surrounding soil.

Fragile remains that are difficult to handle or reassemble can be manipulated repeatedly through virtual representations. Such a process permitted us to reconstruct the face of a young girl from Colonial Jamestown for an exhibition. “Jane” died during the 1609-1610 starving time and pieces of her incomplete skull were found by excavators among refuse deposits. Physically handling the remaining craniofacial bones was possible, but by virtually modeling each of the individual fragments, the bones could be maneuvered in virtual reality until they were effectively reassembled (refit). Missing bones were replaced with mirror images from the opposite side or with virtual pieces replicated from a similar skull from the same time period. The resulting skull was digitally reconstructed into a single unit and reproduced by stereolithography.

The use of 3D printing, or additive manufacturing, of digital models has been used for years to provide a template for facial reconstructions when layered with clay muscles and facial tissues to offer a portrait of the past.

The totally non-invasive, non-destructive nature of the virtopsy approach allows far more in-depth evaluation of fragile or irreplaceable remains. This has particular significance when dealing with human remains where religion or social mores may limit physical examination or sampling.

NMNH forensic anthropologists have had a long history of assisting law enforcement agencies and medical examiners with human identification cases. Evaluation of remains that are not fully skeletonized are frequently CT scanned prior to direct examination. As an example, traumatic throat injuries due to strangulation have been recognized in decomposition cases prior to physical dissection. Nonvisible cartilaginous and osseous structures, such as the hyoid bone and thyroid cartilage, can be initially imaged to check for possible perimortem fractures.

The CT center at NMNH has supported the work for researchers worldwide, with many applications among the studies listed below.

• Canington, S. L. and D. R. Hunt (2016). "Rapid development of secondary hyperparathyroidism and fibrous osteodystrophy in a juvenile orangutan." International Journal of Paleopathology 13: 96-99.
• Carlson, K. J., F. E. Grine and O. M. Pearson (2007). "Robusticity and sexual dimorphism in the postcranium of modern hunter-gatherers from Australia." American Journal of Physical Anthropology 134(1): 9-23.
• Clarke, E. M., R. C. Thompson, A. H. Allam, L. S. Wann, G. P. Lombardi, M. L. Sutherland, J. D. Sutherland, S. L. Cox, M. A.-T. Soliman, G. Abd el-Maksoud, I. Badr, M. I. Miyamoto, B. Frohlich, A.-H. Nur el-din, A. F. R. Stewart, J. Narula, A. R. Zink, C. E. Finch, D. E. Michalik and G. S. Thomas (2014). "Is atherosclerosis fundamental to human aging? Lessons from ancient mummies." Journal of Cardiology 63(5): 329-334.
• Copes, L. E. and W. H. Kimbel (2016). "Cranial vault thickness in primates: Homo erectus does not have uniquely thick vault bones." Journal of Human Evolution 90: 120-134.
• Dunn, R. H., M. W. Tocheri, C. M. Orr and W. L. Jungers (2014). "Ecological divergence and talar morphology in gorillas." American Journal of Physical Anthropology 153(4): 526-541.
• Hunt, D. R. and L. M. Hopper (1996). Non-invasive investigations of human mummified remains by radiographic techniques. Human Mummies: A Global Survey of their Status and the Techniques of Conservation. K. Spindler, H. Wilfing, E. Rastbichler-Zissernig, D. zur Nedden and H. Nothdurfter. Vienna, Springer Vienna: 15-31.
• Jonsdottir, B. and R. D. Medica (2002). "CT scanning of Aleutian mummies." Frohlich B, Harper AB, Gilberg R. To the Aleutians and beyond: the anthropology of William S. Laughlin. Copenhagen: Publications of the National Museum Ethnographic Series 20: 155-167.
• Kallal, R. J., S. J. Godfrey and D. J. Ortner (2012). "Bone reactions on a pliocene cetacean rib indicate short-term survival of predation event." International Journal of Osteoarchaeology 22(3): 253-260.
• Kawashima, T., R. W. Thorington, K. Murakami and F. Sato (2013). "Evolutionary Anatomy and Phyletic Implication of the Extrinsic Cardiac Nervous System in the Philippine Tarsier (Tarsius syrichta, Primates) in Comparisons With Strepsirrhines and New World Monkeys." The Anatomical Record 296(5): 798-806.
• Knigge, R. P., M. W. Tocheri, C. M. Orr and K. P. McNulty (2015). "Three-Dimensional Geometric Morphometric Analysis of Talar Morphology in Extant Gorilla Taxa from Highland and Lowland Habitats." The Anatomical Record 298(1): 277-290.
• Marino, L., D. W. McShea and M. D. Uhen (2004). "Origin and evolution of large brains in toothed whales." The Anatomical Record Part A: Discoveries in Molecular, Cellular, and Evolutionary Biology 281A(2): 1247-1255.
• Marino, L., M. D. Uhen, N. D. Pyenson and B. Frohlich (2003). "Reconstructing cetacean brain evolution using computed tomography." Anat Rec B New Anat 272(1): 107-117.
• McFarlin, S. C., S. K. Barks, M. W. Tocheri, J. S. Massey, A. B. Eriksen, K. A. Fawcett, T. S. Stoinski, P. R. Hof, T. G. Bromage, A. Mudakikwa, M. R. Cranfield and C. C. Sherwood (2013). "Early Brain Growth Cessation in Wild Virunga Mountain Gorillas (Gorilla beringei beringei)." American Journal of Primatology 75(5): 450-463.
• Moreno, K., M. T. Carrano and R. Snyder (2007). "Morphological changes in pedal phalanges through ornithopod dinosaur evolution: A biomechanical approach." Journal of Morphology 268(1): 50-63.
• Owsley, D. W., K. S. Bruwelheide, L. W. Cartmell, L. E. Burgess, S. J. Foote, S. M. Chang and N. Fielder (2006). "The Man in the Iron Coffin: An Interdisciplinary Effort to Name the Past." Historical Archaeology 40(3): 89-108.
• Patel, B. A. and K. J. Carlson (2007). "Bone density spatial patterns in the distal radius reflect habitual hand postures adopted by quadrupedal primates." Journal of Human Evolution 52(2): 130-141.
• Patel, B. A., C. B. Ruff, E. L. R. Simons and J. M. Organ (2013). "Humeral Cross-Sectional Shape in Suspensory Primates and Sloths." The Anatomical Record 296(4): 545-556.
• Pyenson, N. D., J. Vélez-Juarbe, C. S. Gutstein, H. Little, D. Vigil and A. O’Dea (2015). "Isthminia panamensis, a new fossil inioid (Mammalia, Cetacea) from the Chagres Formation of Panama and the evolution of ‘river dolphins’ in the Americas." PeerJ 3: e1227.
• Thompson, R. C., A. H. Allam, G. P. Lombardi, L. S. Wann, M. L. Sutherland, J. D. Sutherland, M. A.-T. Soliman, B. Frohlich, D. T. Mininberg and J. M. Monge (2013). "Atherosclerosis across 4000 years of human history: the Horus study of four ancient populations." The Lancet 381(9873): 1211-1222.
• Thompson, R. C., A. H. Allam, A. Zink, L. S. Wann, G. P. Lombardi, S. L. Cox, B. Frohlich, M. L. Sutherland, J. D. Sutherland, T. C. Frohlich, S. I. King, M. I. Miyamoto, J. M. Monge, C. M. Valladolid, A. el-Halim Nur el-din, J. Narula, A. M. Thompson, C. E. Finch and G. S. Thomas (2014). "Computed Tomographic Evidence of Atherosclerosis in the Mummified Remains of Humans From Around the World." Global Heart 9(2): 187-196.
• Tocheri, M. W., C. R. Solhan, C. M. Orr, J. Femiani, B. Frohlich, C. P. Groves, W. E. Harcourt-Smith, B. G. Richmond, B. Shoelson and W. L. Jungers (2011). "Ecological divergence and medial cuneiform morphology in gorillas." Journal of Human Evolution 60(2): 171-184.
• Yamato, M. and N. D. Pyenson (2015). "Early Development and Orientation of the Acoustic Funnel Provides Insight into the Evolution of Sound Reception Pathways in Cetaceans." PLoS ONE 10(3): e0118582.
• Zuckerman, M. K., E. M. Garofalo, B. Frohlich and D. J. Ortner (2014). "Anemia or scurvy: A pilot study on differential diagnosis of porous and hyperostotic lesions using differential cranial vault thickness in subadult humans." International Journal of Paleopathology 5: 27-33.