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.

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A correlative approach for combining microCT, light and transmission electron microscopy in a single 3D scenario

A correlative approach for combining microCT, light and transmission electron microscopy in a single 3D scenario

In biomedical research, a huge variety of different techniques is currently available for the structural examination of small specimens, including conventional light microscopy (LM), transmission electron microscopy (TEM), confocal laser scanning microscopy (CLSM), microscopic X-ray computed tomography (microCT), and many others. Since every imaging method is physically limited by certain parameters, a correlative use of complementary methods often yields a significant broader range of inform... Read more

Stephan Handschuh, Natalie Baeumler, Thomas Schwaha & Bernhard Ruthensteiner

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3D computational anatomy of the scaphoid and its waist for use in fracture treatment

3D computational anatomy of the scaphoid and its waist for use in fracture treatment

A detailed understanding of scaphoid anatomy helps anatomic fracture reduction and optimal screw position. Therefore, we analyzed the size and shape variations of the cartilage and osseous surface, the distribution of volumetric bone mineral density (vBMD), and if the vBMD values differ between a peripheral and a central screw pathway?

Forty-three fresh frozen hand specimens (17 females, 26 males) were analysed with high-resolution peripheral quantitative computed tomography (HR-pQCT) ... Read more

Marc-Daniel Ahrend, Teun Teunis, Hansrudi Noser, Florian Schmidutz, Geoff Richards, Boyko Gueorguiev & Lukas Kamer

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Analysis of in vitro demineralised human enamel using multi-scale correlative optical and scanning electron microscopy, and high-resolution synchrotron wide-angle X-ray scattering

Analysis of in vitro demineralised human enamel using multi-scale correlative optical and scanning electron microscopy, and high-resolution synchrotron wide-angle X-ray scattering

Enamel caries is a highly prevalent worldwide disease that involves the demineralisation of the outer tooth structure. In this study, we report the analysis of artificially demineralised human enamel sections (‘slices’) etched using lactic acid (2% v/v) in comparison with healthy enamel using correlative techniques of optical and electron microscopy, as well as scanning diffraction. Demineralisation of the enamel was characterised at the micron to sub-micron scale. The structure of the he... Read more

Cyril Besnard, Robert A. Harper, Thomas E. J. Moxham, Jonathan D. James, Malte Storm, Enrico Salvati, Gabriel Landini, Richard M. Shelton, Alexander M.Korsunsky

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3D analysis of enamel demineralisation in human dental caries using high-resolution, large field of view synchrotron X-ray micro-computed tomography

3D analysis of enamel demineralisation in human dental caries using high-resolution, large field of view synchrotron X-ray micro-computed tomography

 

Unprecedented combination of resolution, field of view and contrast for the analysis human enamel carious lesions was achieved. Synchrotron X-ray micro-computed tomography revealed sub-micron details of enamel rod and inter-rod regions inaccessible by laboratory tomography. Successful segmentation and labelling allowed the extraction of enamel etching patterns and statistics. Correlation was obtained between synchrotron X-ray micro-tomography and FIB-SEM cross-sec... Read more

Cyril Besnard, Robert A. Harper, Thomas E. J. Moxham, Jonathan D. James, Malte Storm, Enrico Salvati, Gabriel Landini, Richard M. Shelton, Alexander M.Korsunsky

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Scientists use Avizo to capture the complex dynamics of particle movement in granular materials

Scientists use Avizo to capture the complex dynamics of particle movement in granular materials

Scientists have for the first time captured the complex dynamics of particle movement in granular materials, helping to explain why mixed nuts often see the larger Brazil nuts gather at the top. This phenomenon, known as the ‘Brazil-nut effect’, has huge implications for industries where uneven mixing can critically degrade product quality. The findings could have vital impact on industries struggling with the phenomenon, such as pharmaceuticals and mining.

For th... Read more

Parmesh Gajjar, Chris G. Johnson, James Carr, Kevin Chrispeels, J. M. N. T. Gray & Philip J. Withers

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Pteropods make thinner shells in the upwelling region of the California Current Ecosystem

Pteropods make thinner shells in the upwelling region of the California Current Ecosystem

Shelled pteropods are widely regarded as bioindicators for ocean acidification, because their fragile aragonite shells are susceptible to increasing ocean acidity. While short-term incubations have demonstrated that pteropod calcification is negatively impacted by ocean acidification, we know little about net calcification in response to varying ocean conditions in natural populations. Here, we examine in situ calcification of Limacina helicina pteropods collected from the California... Read more

Lisette Mekkes, Willem Renema, Nina Bednaršek, Simone R. Alin, Richard A. Feely, Jef Huisman, Peter Roessingh & Katja T. C. A. Peijnenburg

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Mitochondria-rough-ER contacts in the liver regulate systemic lipid homeostasis

Mitochondria-rough-ER contacts in the liver regulate systemic lipid homeostasis

In this work, we studied mitochondria-rER contacts in vivo by serial section electron tomography (SSET) and 3D reconstruction analysis of cryo-fixed mouse tissue samples. We characterized this inter-organelle association as mitochondria tightly wrapped by sheets of curved rER (wrappER). Further, we used multi-omics and genetic approaches to obtain evidence that the wrappER is a distinct intracellular compartment and demonstrate the importance of wrappER-mitochondria contacts for v... Read more

Irene Anastasia, Nicolò Ilacqua, Andrea Raimondi, Philippe Lemieux, Rana Ghandehari-Alavijeh, Guilhem Faure, Sergei L. Mekhedov, Kevin J. Williams, Federico Caicci, Giorgio Valle, Marta Giacomello, Ariel D. Quiroga, Richard Lehner, Michael J. Miksis, Katalin Toth, Thomas Q. de Aguiar Vallim, Eugene V. Koonin, Luca Scorrano, Luca Pellegrini

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Porosity and Structure of Hierarchically Porous Ni/Al2O3 Catalysts for CO2 Methanation

Porosity and Structure of Hierarchically Porous Ni/Al2O3 Catalysts for CO2 Methanation

Carbon dioxide emissions must be reduced significantly to limit the negative consequences of climate change. For this reason, fossil fuels must be replaced by renewable energy sources. However, wind and solar energy, for example, are sporadic sources and, thus, not inevitably available when needed. This results in periods of energy surplus and shortage, which are not necessarily predictable. Hence, energy storage concepts are required to compensate for these fluctuations, thereby retaining en... Read more

Sebastian Weber, Ken L. Abel, Ronny T. Zimmermann, Xiaohui Huang, Jens Bremer, Liisa K. Rihko-Struckmann, Darren Batey, Silvia Cipiccia, Juliane Titus, David Poppitz, Christian Kübel, Kai Sundmacher, Roger Gläser, Thomas L. Sheppard

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On structure and mechanics of biomimetic meta-biomaterials fabricated via metal additive manufacturing

On structure and mechanics of biomimetic meta-biomaterials fabricated via metal additive manufacturing

Material synthesis techniques have been historically used to engineer the mechanical and biological properties of biomaterials. Despite the overall success of this approach in different fronts […] there are still major unaddressed challenges due to the limited range of material properties that can be obtained through such synthesis techniques […]. Recent advances in additive manufacturing (AM) have initiated a new paradigm, which could facilitate better control of mechanical and b... Read more

Maryam Tilton, Alireza Borjali, Aaron Isaacson, Kartik Mangudi Varadarajan, Guha P.Manogharan

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Processing and Characterization of Bilayer Materials by Solid State Sintering for Orthopedic Applications

Processing and Characterization of Bilayer Materials by Solid State Sintering for Orthopedic Applications

Nowadays, industrial processes demand materials with specific properties and localized microstructures to improve material performance. To satisfy particular needs, the development of materials with changing mechanical properties and/or microstructures along a preferential direction has been developed. These are called Functional Graded Materials (FGMs). Among these materials, a variation on the porosity along the part is very useful for different industrial applications, such as microfiltrat... Read more

Jorge Sergio Téllez-Martínez, Luis Olmos, Víctor Manuel Solorio-García, Héctor Javier Vergara-Hernández, Jorge Chávez, Dante Arteaga

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Investigating the microstructure and mechanical behaviour of simulant “lava-like” fuel containing materials from the Chernobyl reactor unit 4 meltdown

Investigating the microstructure and mechanical behaviour of simulant “lava-like” fuel containing materials from the Chernobyl reactor unit 4 meltdown

Decommissioning of the damaged Chernobyl nuclear reactor Unit 4 is a top priority for the global community. Before such operations begin, it is crucial to understand the behaviour of the hazardous materials formed during the accident. Since those materials formed under extreme and mostly unquantified conditions, modelling alone is insufficient to accurately predict their physical, chemical and, predominantly, mechanical behaviour. Meanwhile, knowledge of the mechanical characteristics of thos... Read more

C.Paraskevoulakos, J.P.Forna-Kreutzer, K.R.Hallam, C.P.Jones, T.B.Scott, C.Gausse, D.J.Bailey, C.A.Simpson, D.Liu, C.Reinhard, C.L.Corkhill, M.Mostafavi

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SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography

SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID19 pandemic, is a highly pathogenic β-coronavirus. As other coronaviruses, SARS-CoV-2 is enveloped, replicates in the cytoplasm and assembles at intracellular membranes. Here, we structurally characterize the viral replication compartment and report critical insights into the budding mechanism of the virus, and the structure of extracellular virions close to their native state by in situ cryo-electr... Read more

Steffen Klein, Mirko Cortese, Sophie L. Winter, Moritz Wachsmuth-Melm, Christopher J. Neufeldt, Berati Cerikan, Megan L. Stanifer, Steeve Boulant, Ralf Bartenschlager, Petr Chlanda

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Multi-Scale Digital Image Correlation Analysis of In Situ Deformation of Open-Cell Porous Ultra-High Molecular Weight Polyethylene Foam

Multi-Scale Digital Image Correlation Analysis of In Situ Deformation of Open-Cell Porous Ultra-High Molecular Weight Polyethylene Foam

Since its invention and commercialization in the 1950s, ultra-high molecular weight polyethylene (UHMWPE) has been known as a high-performance polymer successfully applied in diverse engineering systems ranging from strong ropes for naval demands and wear-resistant liners in bearings, transportation belts and heavy trucks in mines and quarries, through the lining of chemical vessels and disposable bags in bioreactors, to sophisticated products such as orthopaedic implants and replacements of ... Read more

Eugene S. Statnik, Codrutza Dragu, Cyril Besnard, Alexander J.G. Lunt, Alexey I. Salimon, Aleksey Maksimkin and Alexander M. Korsunsky

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Defect structure process maps for laser powder bed fusion additive manufacturing

Defect structure process maps for laser powder bed fusion additive manufacturing

Accurate detection, characterization, and prediction of defects has great potential for immediate impact in the production of fully-dense and defect free metal additive manufacturing (AM) builds. Accordingly, this paper presents Defect Structure Process Maps (DSPMs) as a means of quantifying the role of porosity as an exemplary defect structure in powder bed printed materials. Synchrotron-based micro-computed tomography (μSXCT) was used to demonstrate that metal AM defects follow predictable... Read more

Jerard V.Gordon, Sneha P.Narra, Ross W.Cunningham, He Liu, Hangman Chen, Robert M.Suter, Jack L.Beuth, Anthony D.Rollett

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A virtual testing platform for filter materials and textile masks

A virtual testing platform for filter materials and textile masks

In order to provide the population with consistent and science-based advice on preferred materials for face masks, we are characterizing the microstructure of different materials using X-ray microfocus computed tomography (microCT), and we use these datasets to simulate the pressure drop (i.e. measure for breathability). We validate our measurements with physically measured filter efficiency and pressure drop, and in this way, we try to develop a “virtual testing platform” for the charac... Read more

The ContrasTTeam of Prof. dr. Greet Kerckhofs, UCLouvain and MTM

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3D characterisation of dry powder inhaler formulations

3D characterisation of dry powder inhaler formulations

Carrier-based dry powder inhaler (DPI) formulations need to be accurately characterised for their particle size distributions, surface roughnesses, fines contents and flow properties. Understanding the micro-structure of the powder formulation is crucial, yet current characterisation methods give incomplete information. Commonly used techniques like laser diffraction (LD) and optical microscopy (OM) are limited due to the assumption of sphericity and can give variable results depending on par... Read more

P. Gajjar, I.D. Styliari, T.T.H. Nguyen, J. Carr, X. Chen, J.A. Elliott, R.B. Hammond, T.L. Burnett, K. Roberts, P.J. Withers, D.Murnane

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Tracking tendon fibers to their insertion – a 3D analysis of the Achilles tendon enthesis in mice

Tracking tendon fibers to their insertion – a 3D analysis of the Achilles tendon enthesis in mice

Tendon insertions to bone are heavily loaded transitions between soft and hard tissues. The fiber courses in the tendon have profound effects on the distribution of stress along and across the insertion. We tracked fibers of the Achilles tendon in mice in micro-computed tomographies and extracted virtual transversal sections. The fiber tracks and shapes were analyzed from a position in the free tendon to the insertion with regard to their mechanical consequences. The fiber number was found to... Read more

Julian Sartori, Heiko Stark

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Neuroanatomical tract-tracing techniques that did go viral

Neuroanatomical tract-tracing techniques that did go viral

Neuroanatomical tracing methods remain fundamental for elucidating the complexity of brain circuits. During the past decades, the technical arsenal at our disposal has been greatly enriched, with a steady supply of fresh arrivals. This paper provides a landscape view of classical and modern tools for tract-tracing purposes. Focus is placed on methods that have gone viral, i.e., became most widespread used and fully reliable.

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Jose L. Lanciego; Floris G. Wouterlood

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Centre of Rotation of the Human Subtalar Joint Using Weight-Bearing Clinical Computed Tomography

Centre of Rotation of the Human Subtalar Joint Using Weight-Bearing Clinical Computed Tomography

The subtalar joint describes an articulation between talus and calcaneus, forming one of two joints of the hindfoot with the tibiotalar or ankle joint above the talus and the subtalar joint below. The talus comprises of three facets (anterior, middle and posterior) that articulate with the mating facets on the calcaneus at the subtalar joint. The bones are connected by a complex of ligamentous structures that connect the talus to the calcaneus and both structures to the adjacent navicular bon... Read more

Marta Peña Fernández, Dorela Hoxha, Oliver Chan, Simon Mordecai, Gordon W. Blunn, Gianluca Tozzi & Andy Goldberg

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An Anisotropic Microstructure Evolution in a Solid Oxide Fuel Cell Anode

An Anisotropic Microstructure Evolution in a Solid Oxide Fuel Cell Anode

A solid oxide fuel cell (SOFC) is an electrochemical device that converts the chemical energy of hydrogen directly into electricity. A single cell usually has a form of a flat plate in which an impervious and dense ion-conducting electrolyte is sandwiched between two porous catalytic electrodes: an anode and a cathode. Fuel is fed to the anode side, and the air is supplied to the cathode. The gasses cannot mix to avoid unproductive combustion. Instead, gasses hit catalyst material, lose their... Read more

Grzegorz Brus, Hiroshi Iwai, Janusz S. Szmyd

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A Neutron Tomographic Analysis of Plated Silver Coins from Ancient Greece Official or Illegal?

A Neutron Tomographic Analysis of Plated Silver Coins from Ancient Greece Official or Illegal?

In the 6th century BC different techniques of coin manufacture were employed by mints in mainland Greece and in the Greek colonies in Southern Italy. In Greece these techniques were evidently derived from the Lydians and consisted in striking a piece of cast metal of predetermined weight (a ‘blank’ or flan) between two engraved dies made of hardened bronze. Colonies in Magna Graecia, however, uniquely developed another set of minting techniques to produce what today is called incuse coina... Read more

Scott Olsen, Filomena Silvemini, Ulf Garbe, Max Avdeev, Joel Davis, Vladimir Luzin, Ken Sheedy

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