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.

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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Using micro-computed tomography to reveal the anatomy of adult Diaphorina citri Kuwayama (Insecta: Hemiptera, Liviidae) and how it pierces and feeds within a citrus leaf

Using micro-computed tomography to reveal the anatomy of adult Diaphorina citri Kuwayama (Insecta: Hemiptera, Liviidae) and how it pierces and feeds within a citrus leaf

The Asian citrus psyllid (ACP), Diaphorina citri, is a harmful pest of citrus trees that transmits Candidatus Liberibacter spp. which causes Huanglongbing (HLB) (citrus greening disease); this is considered to be the most serious bacterial disease of citrus plants.

Here we detail an anatomical study of the external and internal anatomy (excluding the reproductive system) using micro-computed tomography (micro-CT). This is the first complete 3D micro-CT reconstruction o... Read more

Javier Alba-Tercedor, Wayne B. Hunter & Ignacio Alba-Alejandre

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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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High resolution X-ray computed tomography: A versatile non-destructive tool to characterize CFRP-based aircraft composite elements

High resolution X-ray computed tomography: A versatile non-destructive tool to characterize CFRP-based aircraft composite elements

The aim of the current study is to propose a versatile, non-destructive inspection strategy to evaluate the structure of two different aircraft carbon fibre reinforced polymer (CFRP) -based composite configurations, which are widely used for structural elements, respectively layered composite and sandwich structure. X-ray computed tomography (CT) has been used as a flexible method for assessment of porosity levels in CFRP components in both types of configuration, permitting to investigate th... Read more

Elena Dilonardo, Michele Nacucchi, Fabio De Pascalis, Mauro Zarrelli, Cinzia Giannini

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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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High-speed synchrotron X-ray imaging of glass foaming and thermal conductivity simulation

High-speed synchrotron X-ray imaging of glass foaming and thermal conductivity simulation

Glass foams are attractive thermal insulation materials, thus, the thermal conductivity (λ) is crucial for their insulating performance. Understanding the foaming process is critical for process optimization. Here, we applied high-speed synchrotron X-ray tomography to investigate the change in pore structure during the foaming process, quantifying the foam structures and porosity dynamically. The results can provide guidance for the manufacturing of glass foams. The 3D pore structures were a... Read more

Martin B. Østergaard, Manlin Zhang, Xiaomei Shen, Rasmus R. Petersen, Jakob König, Peter D. Lee, Yuanzheng Yue, Biao Cai

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Revealing the mechanisms by which magneto-hydrodynamics disrupts solidification microstructures

Revealing the mechanisms by which magneto-hydrodynamics disrupts solidification microstructures

A key technique for controlling solidification microstructures is magneto-hydrodynamics (MHD), resulting from imposing a magnetic field to solidifying metals and alloys. Applications range from bulk stirring to flow control and turbulence damping via the induced Lorentz force. Over the past two decades the Lorentz force caused by the interaction of thermoelectric currents and a magnetic field, a MHD phenomenon known as Thermoelectric Magnetohydrodynamics (TEMHD), was also shown to drive inter... Read more

B. Cai, A. Kao, E. Boller, O.V. Magdysyuk, R.C. Atwood, N.T. Vo, K. Pericleous, P.D. Lee

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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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Membrane architecture of pulmonary lamellar bodies revealed by post-correlation on-lamella cryo-CLEM

Membrane architecture of pulmonary lamellar bodies revealed by post-correlation on-lamella cryo-CLEM

Lamellar bodies (LBs) are surfactant rich organelles in alveolar type 2 cells. LBs disassemble into a lipid-protein network that reduces surface tension and facilitates gas exchange at the air-water interface in the alveolar cavity. Current knowledge of LB architecture is predominantly based on electron microscopy studies using disruptive sample preparation methods. We established a post-correlation on-lamella cryo-correlative light and electron microscopy approach for cryo-FIB milled lung ce... Read more

Steffen Klein, Benedikt H. Wimmer, Sophie L. Winter, Androniki Kolovou, Vibor Laketa, Petr Chlanda

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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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X-ray Micro-Computed Tomography of Polymer Electrolyte Fuel Cells: What is the Representative Elementary Area?

X-ray Micro-Computed Tomography of Polymer Electrolyte Fuel Cells: What is the Representative Elementary Area?

With the growing use of X-ray computed tomography (X-ray CT) datasets for modelling of transport properties, comes the need to define the representative elementary volume (REV) if considering three dimensions or the representative elementary area (REA) if considering two dimensions. The resolution used for imaging must be suited to the features of interest in the sample and the region-of-interest must be sufficiently large to capture key information. Polymer electrolyte fuel cells have a hier... Read more

Jennifer Hack et al 2020 J. Electrochem.

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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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Microstructure Characterization by X-Ray Computed Tomography of C/C-SiC Ceramic Composites Fabricated with Different Carbon Fiber Architectures

Microstructure Characterization by X-Ray Computed Tomography of C/C-SiC Ceramic Composites Fabricated with Different Carbon Fiber Architectures

The microstructure morphologies have been characterized by high resolution laboratory X-ray computed tomography in Carbon Fiber Reinforced Carbon and Silicon Carbide (C/C-SiC) ceramic composites fabricated by Gaseous Silicon Infiltration (GSI) from C/C preforms of three different architectures: 3D stitched cloth fabric; 3D orthogonal woven fabric; and needled short-cut felt. Each composites’ microstructure was influenced by the structure of the C/C preform. By incorporating tomography with ... Read more

Fan Wan, Talha, J. Pirzada, Rongjun Liu, Yanfei Wang, Changrui Zhang, Thomas James Marrow

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Impact of Pore Tortuosity on Electrode Kinetics in Lithium Battery Electrodes: Study in Directionally Freeze-Cast LiNi0.8Co0.15Al0.05O2 (NCA)

Impact of Pore Tortuosity on Electrode Kinetics in Lithium Battery Electrodes: Study in Directionally Freeze-Cast LiNi0.8Co0.15Al0.05O2 (NCA)

The prevailing electrode fabrication method for lithium-ion battery electrodes includes calendering at high pressures to densify the electrode and promote adhesion to the metal current collector.

However, this process increases the tortuosity of the pore network in the primary transport direction and imposes severe tradeoffs between electrode thickness and rate capability. With the aim of understanding the impact of pore tortuosity on electrode kinetics, and enabling cell designs with ... Read more

Benjamin Delattre, Ruhul Amin, Jonathan Sander, Joël De Coninck, Antoni P. Tomsia and Yet-Ming Chiang

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Three-dimensional assessment of enamel and dentine in mouse molar teeth during masseter muscle hypofunction

Three-dimensional assessment of enamel and dentine in mouse molar teeth during masseter muscle hypofunction

Mouse molar is a widely used model for teeth development. However, the effect of masticatory function on enamel and dentine in adult individuals remains poorly understood. As reported, the unilateral masseter hypofunction induced by botulinum toxin type A (BoNTA) resulted in mandibular bone damage and signs of unilateral chewing in adult mice.

Enamel volume from treated side resulted unchanged after 2 weeks of unilateral masseter hypofunction. No differences for enamel volume were fou... Read more

Julián BALANTA-MELO, Maximilian BEMMANN, Viviana TORO-IBACACHE, Kornelius KUPCZIK, Sonja BUVINIC

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Utilization of Recycled Material Sources for Wood-Polypropylene Composites: Effect on Internal Composite Structure, Particle Characteristics and Physico-Mechanical Properties

Utilization of Recycled Material Sources for Wood-Polypropylene Composites: Effect on Internal Composite Structure, Particle Characteristics and Physico-Mechanical Properties

In this study, various wood material sources were used for the manufacture of wood-polymer composites (WPC). The materials were categorised as virgin wood particles (VWP), reprocessed WPC particles (RWP) and recycled thermoset composite particles (RCP) and derived from two virgin wood sources, three-layer particle boards, medium-density fibre boards (MDF) boards,or two different wood/polypropylene composites. All produced wood-polypropylene compounds contained 60% wood material and were manu... Read more

Kim Christian Krause, D, Philipp Sauerbier, Tim Koddenberg and Andreas Krause

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The effect of wetting area in carbon paper electrode on the performance of vanadium redox flow batteries: A three-dimensional lattice Boltzmann study

The effect of wetting area in carbon paper electrode on the performance of vanadium redox flow batteries: A three-dimensional lattice Boltzmann study

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

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Towards digital metal additive manufacturing via high-temperature drop-on-demand jetting

Towards digital metal additive manufacturing via high-temperature drop-on-demand jetting

Drop-on-demand jetting of metals offers a fully digital manufacturing approach to surpass the limitations of the current generation powder-based additive manufacturing technologies. However, research on this topic has been restricted mainly to near-net shaping of relatively low melting temperature metals. Here it is proposed a novel approach to jet molten metals at high-temperatures (>1000 °C) to enable the direct digital additive fabrication of micro- to macro-scale objects. […] ... Read more

Marco Simonelli, Nesma Aboulkhair, Mircea Rasa, Mark East, Chris Tuck, Ricky Wildman, Otto Salomons, Richard Hague

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High-resolution mapping of brain vasculature and its impairment in the hippocampus of Alzheimer’s disease mice

High-resolution mapping of brain vasculature and its impairment in the hippocampus of Alzheimer’s disease mice

Accumulating evidence indicates the critical importance of cerebrovascular dysfunction in the pathogenesis of Alzheimer’s disease (AD). However, systematic comparative studies on the precise brain vasculature of wild-type and AD model mice are still rare. Using an image optimization method for analyzing Micro-Optical Sectioning Tomography (MOST) data, we generated cross-scale whole-brain 3D atlases that cover the entire vascular system from large vessels down to smallest capillaries at ... Read more

Xiaochuan Zhang, Xianzhen Yin, Jingjing Zhang, Anan Li, Hui Gong, Qingming Luo, Haiyan Zhang, Zhaobing Gao, Hualiang Jiang

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Morphological evolution and internal strain mapping of pomelo peel using X-ray computed tomography and digital volume correlation

Morphological evolution and internal strain mapping of pomelo peel using X-ray computed tomography and digital volume correlation

Among natural cellular materials, pomelo peels, having a foam-like hierarchical microstructure, represent an ideal model for developing materials with high energy absorption efficiency. In this work, by combining X-ray tomographic imaging technique and digital volume correlation (DVC), in-situ stepwise uniaxial compression tests were performed to quantify the internal morphological evolution and kinematic responses of pomelo peel samples during compression.

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B.Wang, B.Pan, G.Lubineau

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