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 Amira-Avizo Software 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.

Juvenile Ovine Ex Vivo Larynges: Phonatory, Histologic, and Micro CT Based Anatomic Analyses

Juvenile Ovine Ex Vivo Larynges: Phonatory, Histologic, and Micro CT Based Anatomic Analyses

It is well known that the phonatory process changes during the life span. However, detailed investigations on potential factors concerned are rare. To deal with this issue, we performed extended biomechanical, macro anatomical, and histological analyses of the contributing laryngeal structures in ex vivo juvenile sheep models. Altogether twelve juvenile sheep larynges were analyzed within the phonatory experiments. Three different elongation levels and 16 different flow levels were applied to... Read more

Michael Döllinger, Olaf Wendler, Claus Gerstenberger, Tanja Grossmann, Marion Semmler, Hossein Sadeghi, and Markus Gugatschka

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UCSF School of Dentistry uses Avizo software to extract changes in periodontal ligament space and tooth movement due to orthodontic therapy

UCSF School of Dentistry uses Avizo software to extract changes in periodontal ligament space and tooth movement due to orthodontic therapy

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

Kyle H.-Y. Chan, fourth-year undergraduate student in Molecular and Cell Biology, and Public Health at UC Berkeley, FeiFei Yang, Ph.D., postdoctoral scholar in the Laboratory of Multiscale Biomechanics and Biomineralization, School of Dentistry, UCSF, and Sunita P. Ho, Ph.D., Division of Biomaterials and Bioengineering, Department of Preventive and Restorative Dental Sciences, School of Dentistry, University of California San Francisco

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The Manufacturing Technology Centre (MTC) uses Avizo to quantify potential defects in additively manufactured samples

The Manufacturing Technology Centre (MTC) uses Avizo to quantify potential defects in additively manufactured samples

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

Dr Shuai Hou, Mélanie Bombardiere, Nathanael Turner, Jonathan Settle, Emmanuel Muzangaza, Dr David Brackett

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GEVES uses Avizo software to study and control plant seeds

GEVES uses Avizo software to study and control plant seeds

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

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Ghassen Trigui, Laurence Le Corre, Dominique Honoré and Karima Boudehri-Giresse - 2D/3D Imaging - R&D team, GEVES

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Pushing the limits of neutron tomography in palaeontology: Three-dimensional modelling of in situ resin within fossil plants

Pushing the limits of neutron tomography in palaeontology: Three-dimensional modelling of in situ resin within fossil plants

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

Chris Mays, Joseph J. Bevitt, and Jeffrey D. Stilwell

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A virtual world of paleontology

A virtual world of paleontology

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.

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Trends in Ecology & Evolution

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2 BILLION years old fossils appear to represent a first experiment in megascopic multicellularity

2 BILLION years old fossils appear to represent a first experiment in megascopic multicellularity

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

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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

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

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Immunofluorescence Tomography: High-resolution 3-D reconstruction by serial-sectioning of methacrylate embedded tissues and alignment of 2-D immunofluorescence images

Immunofluorescence Tomography: High-resolution 3-D reconstruction by serial-sectioning of methacrylate embedded tissues and alignment of 2-D immunofluorescence images

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

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Modelling deformation and fracture in confectionery wafers

Modelling deformation and fracture in confectionery wafers

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

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3D Muscle Architecture of the Pectoral Muscles of European Starling (Sturnus vulgaris)

3D Muscle Architecture of the Pectoral Muscles of European Starling (Sturnus vulgaris)

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

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Testing hypotheses for the function of the carnivoran baculum using finite-element analysis

Testing hypotheses for the function of the carnivoran baculum using finite-element analysis

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

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Microbial-tubeworm associations in a 440 million year old hydrothermal vent community

Microbial-tubeworm associations in a 440 million year old hydrothermal vent community

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

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Caudals and Calyces: The Curious Case of a Consumed Chiapan Colubroid

Caudals and Calyces: The Curious Case of a Consumed Chiapan Colubroid

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

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Comparative Morphology of the Internal Nasal Skeleton of Adult Marsupials Based on X-ray Computed Tomography

Comparative Morphology of the Internal Nasal Skeleton of Adult Marsupials Based on X-ray Computed Tomography

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

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Investigation of Hot Pressed Polymer Electrolyte Fuel Cell Assemblies via Xray Computed Tomography

Investigation of Hot Pressed Polymer Electrolyte Fuel Cell Assemblies via Xray Computed Tomography

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

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Fatigue of short fibre reinforced polymers: from material process to fatigue life of industrial components

Fatigue of short fibre reinforced polymers: from material process to fatigue life of industrial components

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

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Damage Evaluation in Woven Glass Reinforced Polyamide 6.6/6 Composites Using Ultrasound Phase-Shift Analysis and X-ray Tomography

Damage Evaluation in Woven Glass Reinforced Polyamide 6.6/6 Composites Using Ultrasound Phase-Shift Analysis and X-ray Tomography

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

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Influence of the rheological properties on the steel fibre distribution and orientation in self-compacting concrete

Influence of the rheological properties on the steel fibre distribution and orientation in self-compacting concrete

The interest in potential applications produced with self-compacting fibre reinforced concrete continues to grow, but in practice, problems associated with an uneven distribution and orientation of fibres in the concrete structure occur. It is not clear what exactly influences uneven distribution of fibres in selfcompacting concrete (SCC) mixtures, especially during the casting and how different factors influence fibre orientation. The objective of this work was to investigate how rheological... Read more

Elena Jasiuniene, Vaidotas Cicenas, Paulius Grigaliunas, Zymantas Rudzionis, Arunas Aleksandras Navickas

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Determination of steel fibres distribution in self-compacting concrete beams using X-ray computed tomography

Determination of steel fibres distribution in self-compacting concrete beams using X-ray computed tomography

In this paper a study concerning an automatic determination of distribution of steel fibres in self-compacting concrete (SCC) is presented. The determination of fibre distribution is required to assess any relationship between those features and casting methods of concrete elements. Concrete beams with steel fibres of various types and casting methods were examined. Involved methods were computed tomography imaging followed by image analysis. After image analysis a label map consisting of all... Read more

T. Ponikiewski, J. Golaszewski, M. Rudzki, M. Bugdol

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Observing the devastating coffee berry borer (Hypothenemus hampei) inside the coffee berry using microcomputed tomography

Observing the devastating coffee berry borer (Hypothenemus hampei) inside the coffee berry using microcomputed tomography

The coffee berry borer is the most devastating insect pest of coffee throughout the world. The insect spends most of its life cycle inside the coffee berry, which makes it quite difficult to observe its behaviour. Micro-computed tomography (micro-CT) was used to observe all developmental stages of the coffee berry borer inside coffee berries (Coffea canephora). An interesting oviposition pattern involving a sequential placement of eggs starting in the periphery of the seed and moving inwards ... Read more

Ignacio Alba-Alejandre, Javier Alba-Tercedor, Fernando E. Vega

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