Welcome to the Amira-Avizo Software Use Case Gallery
Below you will find a collection of use cases of our 3D data visualization and analysis software. These use cases include scientific publications, articles, papers, posters, presentations or even videos that show how is used to address various scientific and industrial research topics.
Use the Domain selector to filter by main application area, and use the Search box to enter keywords related to specific topics you are interested in.
The appearance of wings in insects, early in their evolution , 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 . 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
Department of Zoology, Faculty of Science, Charles University, Praha, Czech Republic and al.
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.Read more
Trends in Ecology & Evolution
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
Abderrazak El Albani, Laboratoire HYDRASA, UMR 6269 CNRS-INSU, Université de Poitiers, France
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
Hsin-Chung Cheng, Boe-Yu Peng, May-Show Chen, Chiung-Fang Huang, Yi Lin, and Yung-Kang Shen
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
Gang Zhou, Qi Zhang, Ruonan Baiand, Guanhua Ni
Under the armor: X-ray computed tomographic reconstruction of the internal skeleton of Coahomasuchus chathamensis (Archosauria: Aetosauria) from the Upper Triassic of North Carolina, USA, and a phylogenetic analysis of Aetosauria
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
Devin K. Hoffman, Andrew B. Heckert, Lindsay E. Zanno
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
Laurie Verzeaux, Nicolas Belloy, Jessica Thevenard-Devy, Jérôme Devy, Géraldine Ferracci, Laurent Martiny, Stéphane Dedieu, Manuel Dauchez, Hervé Emonard, Nicolas Etique & Emmanuelle Devarenne-Charpentier
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
Parfitt, Geraint J
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
Idris K. Mohammeda, Maria N. Charalambides , J. Gordon Williams , John Rasburn
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
S.P. Sullivan, F.R. McGechie, K.M. Middleton, C.M. Holliday
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
Charlotte A. Brassey, James D. Gardiner, and Andrew C. Kitchener
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
Magdalena N. Georgieva , Crispin T. S. Little , Russell J. Bailey , Alexander D. Ball and Adrian G. Glover
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
Jonathan A. Campbell, Eric N. Smith, and Alexander S. Hall
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
Thomas E. Macrini
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
Achim H Schwermann, Tomy dos Santos Rolo, Michael S Caterino, Gunter Bechly, Heiko Schmied, Tilo Baumbach, Thomas van de Kamp
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
STEVEN R. MANCHESTER, BEHNAZ BALMAKI
The hot pressing process for fabricating membrane electrode assemblies (MEAs) has been widely adopted, yet little is known of its effects on the microstructural properties of the different components of the MEA. In particular, the interaction of the electrolyte, electrode and gas diffusion layer (GDL) due to lamination is difficult to probe as conventional imaging techniques cannot access the internal structure of the MEA. Here, a novel approach is used, which combines characterisation of hot... Read more
Q. Meyer, N. Mansor, F. Iacoviello, P.L. Cullen, R. Jervis, D. Finegan, C. Tan, J. Bailey, P. R. Shearing, D. J. L. Brett
For many years, SFRPs (short fibre reinforced polyamides) have been used in the automotive industry as a means to reduce vehicle weight. However, their complex anisotropic and heterogeneous microstructure requires sophisticated material characterisation and simulation. This study aims at presenting the simulation strategy adopted by an automotive company address these challenges. The manufacturing process is first simulated and correlated with tomography analysis. Then, based on the numerical... Read more
Pablo Wilson, Peter Heyes
The paper proposes a new experimental methodology, based on ultrasonic measurements, that aims at evaluating the anisotropic damage in woven semi-crystalline polymer composites through new damage indicators. Due to their microstructure, woven composite materials are characterized by an anisotropic evolution of damage induced by different damage mechanisms occurring at the micro or mesoscopic scales. In this work, these damage modes in polyamide 6.6/6-woven glass fiber reinforced composites ha... Read more
Pascal Pomarède, Fodil Meraghni, Laurent Peltier, Stéphane Delalande, Nico F. Declercq
The vanadium redox flow battery (VRFB) has emerged as a promising technology for large-scale storage of intermittent power generated from renewable energy sources due to its advantages such as scalability, high energy efficiency and low cost. In the current study, a three-dimensional(3D) Lattice Boltzmann model is developed to simulate the transport mechanisms of electrolyte flow, species and charge in the vanadium redox flow battery at the micro pore scale. An electrochemical model using the... Read more
Duo Zhang, Qiong Cai, Oluwadamilola O.Taiwo, Vladimir Yufit, Nigel P.Brandon, Sai Gu