Welcome to the Amira-Avizo Software Use Case Gallery

During the acts of biting and chewing, the muscles of the jaw (consisting of the masseter, temporalis, and medial pterygoid in the elevator group, and lateral pterygoid as the main depressor) generate forces that dictate jaw kinematics . The movement of jaws hinges about the temporomandibular joint and are brought together by the muscles attached to respective bones through bone-tendon interfaces known as entheses . Thus, chewing forces affect aspects of craniofacial structure as well as bo... Read more

Electron Beam Melting (EBM) is an Additive Manufacturing (AM) process which can be used to fabricate complex 3D metal components. Ti-6Al-4V is one of the high value aerospace materials that has been widely used in the EBM process. However, defects such as gas pores and lack of fusion are often found in the as-built components, which can make a significant difference to the fatigue resistance of the parts. The Manufacturing Technology Centre (MTC) uses X-ray Computed Tomography (XCT) and 3D im... Read more

At GEVES, Microtomography (micro-CT), which is a technique using X-rays to investigate internal anatomy and morphology of organisms without destruction, is applied to plant seed quality control and phenotyping. Several applications have been developed using micro-CT coupled with Avizo software development, such as for example in the Measurements of internal and external sugar beet seed structures for seed phenotyping

Computed tomography is an increasingly popular technique for the non-destructive study of fossils. Whilst the science of X-ray computed tomography (CT) has greatly matured since its first fossil applications in the early 1980s, the applications and limitations of neutron tomography (NT) remain relatively unexplored in palaeontology. These highest resolution neutron tomographic scans in palaeontology to date were conducted on a specimen of Austrosequoia novae-zeelandiae (Ettingshausen) Mays an... Read more

The appearance of wings in insects, early in their evolution [1], has been one of the more critical innovations contributing to their extraordinary diversity. Despite the conspicuousness and importance of wings, the origin of these structures has been difficult to resolve and represented one of the “abominable mysteries” in evolutionary biology [2]. More than a century of debate has boiled the matter down to two competing alternatives—one of wings representing an extension of the thorac... Read more

Computer-aided visualization and analysis has revolutionized the study of fossils. Fossils can now be characterized in three dimensions and in unprecedented detail. The resulting digital reconstructions can be used in rigorous functional analyses. Hypotheses regarding the function of extinct organisms can therefore be tested.

The Paleoproterozoic Era witnessed crucial steps in the evolution of Earth’s surface environments following the first appreciable rise of free atmospheric oxygen concentrations ∼2.3 to 2.1 Ga ago, and concomitant shallow ocean oxygenation. Combined microtomography, geochemistry, and sedimentary analysis suggest a biota fossilized during early diagenesis. The emergence of this biota follows a rise in atmospheric oxygen, which is consistent with the idea that surface oxygenation allowe... Read more

Endosseous oral implant is applied for orthodontic anchorage in subjects with multiple tooth agenesis. Its effectiveness under orthodontic loading has been demonstrated clinically and experimentally. This study investigates the deformation and stress on the bone and implant for different bite forces by three-dimensional (3D) finite element (FE) methods. A numerical simulation of deformation and stress distributions around implants was used to estimate the survival life for implants. The model... Read more

This paper used the X-ray three-dimensional (3D) microscope and acquired, through CT scanning, the 3D data of the long-frame coal sample from the Daliuta Coal Mine.

Then, the 3D datacube reconstructed from the coal’s CT scanning data was visualized with the use of Avizo, an advanced visualization software. By means of a gray-scale segmentation technique, the model of the coal’s micro-pore structure was extracted from the object region, and the precise characterization was then cond... Read more

Aetosauria is a clade of heavily armored, quadrupedal omnivorous to herbivorous archosaurs known from the Late Triassic across what was the supercontinent of Pangea. Their abundance in many deposits relative to the paucity of other Triassic herbivores indicates that they were key components of Late Triassic ecosystems. However, their evolutionary relationships remain contentious due, in large part, to their extensive dermal armor, which often obstructs observation of internal skeletal anatomy... Read more

The tissue inhibitor of metalloproteinases-1 (TIMP-1) exerts inhibitory activity against matrix metalloproteinases and cytokine-like effects. We previously showed that TIMP-1 reduces neurite outgrowth in mouse cortical neurons and that this cytokine-like effect depends on TIMP-1 endocytosis mediated by the low-density lipoprotein receptor-related protein-1 (LRP-1). To gain insight into the interaction between TIMP-1 and LRP-1, we considered conformational changes that occur when a ligand bind... Read more

Immunofluorescence tomography is a high-resolution 3-D reconstruction method based on methacrylate embedding and serial-sectioning, where 2-D images of immuno-stained serial-sections are computationally aligned into image stacks, and the 3-D volume rendered. Butyl-Methyl Methacrylate (BMMA) plastic was adopted as it preserves excellent tissue morphology and can be de-plasticized easily using an organic solvent, which enables immuno-staining of serial-sections without antibody penetration issu... Read more

The aim of this research is to model the deformation and fracture behaviour of brittle wafers often used in chocolate confectionery products.

Three point bending and compression experiments were performed on beam and circular disc samples respectively to determine the ‘apparent’ stress-strain curves in bending and compression. The deformation of the wafer for both these testing types was observed in-situ within an SEM. The wafer is modelled analytically and numerically as a composi... Read more

Avian flight is achieved through a number of modifications to the body, including the pectoral girdle (…). Muscle architecture is a critical variable in determining the biomechanical function of the vertebrate musculoskeletal system; however, accurate three-dimensional (3D) understanding of muscle architecture has been historically difficult to acquire. Here, we present a musculoskeletal model of a European starling (Sturnus vulgaris) pectoral girdle generated from iodine contr... Read more

The baculum (os penis) is a mineralized bone within the glans of the mammalian penis and is one of the most morphologically diverse structures in the mammal skeleton. (…) For the first time, to our knowledge, we apply a computational simulation approach (finite-element analysis; FEA) to quantify the three-dimensional biomechanical performance of carnivoran bacula (n = 74) based upon high-resolution micro-computed tomography scans. (…) a highly significant negative relation... Read more

Microorganisms are the chief primary producers within present-day deep-sea hydrothermal vent ecosystems, and play a fundamental role in shaping the ecology of these environments. (…) The oldest known hydrothermal vent community that includes metazoans is preserved within the Ordovician to early Silurian Yaman Kasy massive sulfide deposit, Ural Mountains, Russia. (…) A re-examination of these fossils using a range of microscopy, chemical analysis and nano-tomography techniques re... Read more

A new genus and species of colubroid snake is described from the isolated highlands of western Chiapas. This enigmatic little snake possesses a unique suite of characters that defies placing it in any known genus and clearly distinguishes it from all known genera. Several of the most unusual features include subcaudals undivided throughout the length of the tail and a simple hemipenis completely adorned with calyces and having a sulcus spermaticus that remains unbifurcated until the apical po... Read more

The internal skeleton of the nasal cavity is sporadically and often incompletely described for many marsupial species and mammals in general. Here, I provide an anatomical survey of the ethmoid in the skulls of adult marsupials based on examination of computed tomography (CT) imagery of 29 taxa representing all the major extant groups of marsupials. (…) I compared ecological data with the number of ecto- and endoturbinals as a preliminary test to determine whether some of the interspec... Read more

External and internal morphological characters of extant and fossil organisms are crucial to establishing their systematic position, ecological role and evolutionary trends. (…) We found well-preserved three-dimensional anatomy in mineralized arthropods from Paleogene fissure fillings and demonstrate the value of these fossils by utilizing digitally reconstructed anatomical structure of a hister beetle. The new anatomical data facilitate a refinement of the species diagnosis and allowed... Read more

PhD student Jesse Hennekam wins for his reconstruction of the skull of a giant dormouse.

A York PhD student has won a prestigious award for his work reconstructing the skull of a giant rodent.

Jesse Hennekam, from the Centre for Anatomical and Human Sciences at the Hull York Medical School, created a digital reconstruction of the skull of a gigantic dormouse (Leithia melitensis), which roamed on the island of Sicily during the Pleistocene, roughly 2 million years ago... Read more

Fossil fruits formerly described as cashews from the Oligocene of Peru are reinvestigated based on the original specimens and newly collected materials. The recovery of an outer spiny layer, preserved in the sedimentary molds surrounding the locule casts, indicates that these disseminules do not represent Anacardium. Imagery from nano-CT scans of the specimens documents a distinctive morphology which does not resemble any fruits or seeds of Anacardiaceae. We describe the morphology in more de... Read more