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.

A statistical assessment of ductile damage in 304L stainless steel resolved using X-ray computed tomography

A statistical assessment of ductile damage in 304L stainless steel resolved using X-ray computed tomography

X-ray computed tomography (XCT) has been shown to reveal the true extent of ductile damage below the fracture surface of failed test specimens, which is often significantly underestimated when probed using 2D serial sectioning techniques and a microscope, since a single plane of material may only exhibit only a handful of resolvable voids.

In contrast XCT offers the capability to generate large datasets consisting of hundreds, if not thousands, of individually resolvable voids, where e... Read more

A. J. Cooper ; O. C. G. Tuck ; T. L. Burnett ; A. H. Sherry

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Investigating microstructural evolution during the electroreduction of UO2 to U in LiCl-KCl eutectic using focused ion beam tomography

Investigating microstructural evolution during the electroreduction of UO2 to U in LiCl-KCl eutectic using focused ion beam tomography

Reprocessing of spent nuclear fuels using molten salt media is an attractive alternative to liquid-liquid extraction techniques.

Pyroelectrochemical processing utilizes direct, selective, electrochemical reduction of uranium dioxide, followed by selective electroplating of a uranium metal. Thermodynamic prediction of the electrochemical reduction of UO2 to U in LiCl-KCl eutectic has shown to be a function of the oxide ion activity. The pO2 of the salt may be affected by the microstruc... Read more

L.D. Brown, R. Abdulaziz, B. Tjaden, D. Inman, D.J.L. Brett, P.R. Shearing

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Nuclear waste viewed in a new light; a synchrotron study of uranium encapsulated in grout

Nuclear waste viewed in a new light; a synchrotron study of uranium encapsulated in grout

How do you characterise the contents of a sealed nuclear waste package without breaking it open?

This question is important when the contained corrosion products are potentially reactive with air and radioactive. Synchrotron X-rays have been used to perform micro-scale in-situ observation and characterisation of uranium encapsulated in grout; a simulation for a typical intermediate level waste storage packet. X-ray tomography and X-ray powder diffraction generated both qualitative and ... Read more

C.A. Stitt, M. Hart, N.J. Harker, K.R. Hallam, J. MacFarlane, A. Banos, C. Paraskevoulakos, E. Butcher, C. Padovani, T.B. Scott

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Human Motor Thalamus Reconstructed in 3D from Continuous Sagittal Sections with Identified Subcortical Afferent Territories

Human Motor Thalamus Reconstructed in 3D from Continuous Sagittal Sections with Identified Subcortical Afferent Territories

Classification and delineation of the motor-related nuclei in the human thalamus have been the focus of numerous discussions for a long time. Difficulties in finding consensus have for the most part been caused by paucity of direct experimental data on connections of individual nuclear entities. Kultas-Ilinsky et al. (2011, J Comp Neurol, 519:2811-2837) showed that distribution of the isoform 65 of glutamic acid decarboxylase (GAD65), the enzyme that synthesizes inhibitory neurotransmitt... Read more

Igor Ilinsky, Andreas Horn, Perrine Paul-Gilloteaux, Pierre Gressens, Catherine Verney, Kristy Kultas-Ilinsky

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Seeing through nuclear fuel: Three-dimensional, nondestructive X-ray microscopy and volumetric analyses of neutron-irradiated TRISO-coated fuel kernels

Seeing through nuclear fuel: Three-dimensional, nondestructive X-ray microscopy and volumetric analyses of neutron-irradiated TRISO-coated fuel kernels

The three-dimensional (3D) characterization of nuclear fuel with X-ray microscopy has historically proven difficult, due to uranium’s high attenuation of easily accessible X-rays, both in a laboratory setting and at a synchrotron user facility. However, this imaging modality provides nondestructive information that can be used to investigate morphological changes arising from external stimuli (e.g., neutron irradiation, high-temperature testing).

Using an appropriate X-ray energy spe... Read more

Nikolaus L. Cordes, William C. Chuirazzi & Joshua J. Kane - John D. Stempien

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Real time, in-situ deuteriding of uranium encapsulated in grout; effects of temperature on the uranium-deuterium reaction

Real time, in-situ deuteriding of uranium encapsulated in grout; effects of temperature on the uranium-deuterium reaction

To accurately predict the initiation and evolution of uranium hydride potentially present in nuclear waste containers, studies of simulated conditions are required.

Here, for the first time, the uranium-deuterium reaction was examined in-situ, in real time, whilst within grouted media. A deuterium gas control rig and stainless steelquartz glass reaction cell were configured on a synchrotron beam line to collect X-ray diffraction and X-ray tomography data. It was found that deuteride fo... Read more

C.A. Stitt, C. Paraskevoulakos, N.J. Harker, A. Banos, K.R. Hallam, C.P. Jones, T.B. Scott

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A multi-scale three-dimensional Cellular Automata fracture model of radiolytically oxidised nuclear graphite

A multi-scale three-dimensional Cellular Automata fracture model of radiolytically oxidised nuclear graphite

A multi-scale approach for fracture simulation, based on the Cellular Automata technique, has been developed and then applied to a nuclear graphite that is used in structural components of the UK Advanced Gas-cooled Reactors (AGR).

High resolution X-ray computed tomographs of Gilsocarbon grade
graphite, with up to 68% weight loss by radiolytic oxidation, provide quantitative descriptions of the porosity within its constitutive filler particles and their surrounding matrix. The st... Read more

Yelena Vertyagina, Thomas James Marrow

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In situ observation of mechanical damage within a SiC-SiC ceramic matrix composite

In situ observation of mechanical damage within a SiC-SiC ceramic matrix composite

SiC-SiC ceramic matrix composites are candidate materials for fuel cladding in Generation IV nuclear fission reactors and as accident tolerant fuel clad in current generation plant.

Experimental methods are needed that can detect and quantify the development of mechanical damage, to support modelling and qualification tests for these critical components. In situ observations of damage development have been obtained of tensile and C-ring mechanical test specimens of a braided nuclear gr... Read more

L. Saucedo-Mora, T. Lowe, S. Zhao, P.D. Lee, P.M. Mummery, T.J. Marrow

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Microstructural analysis of TRISO particles using multi-scale X-ray computed tomography

Microstructural analysis of TRISO particles using multi-scale X-ray computed tomography

TRISO particles, a composite nuclear fuel built up by ceramic and graphitic layers, have outstanding high temperature resistance. TRISO fuel is the key technology for High Temperature Reactors (HTRs) and the Generation IV Very High Temperature Reactor (VHTR) variant.

TRISO offers unparalleled containment of fission products and is extremely robust during accident conditions. An understanding of the thermal performance and mechanical properties of TRISO fuel requires a detailed knowledg... Read more

T. Lowe, R.S. Bradley, S. Yue, K. Barii, J. Gelb, N. Rohbeck, J. Turner, P.J. Withers

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Hyperpolarized 13C MR metabolic imaging can detect neuroinflammation in vivo in a multiple sclerosis murine model

Hyperpolarized 13C MR metabolic imaging can detect neuroinflammation in vivo in a multiple sclerosis murine model

Proinflammatory mononuclear phagocytes (MPs) play a crucial role in the progression of multiple sclerosis (MS) and other neurodegenerative diseases. Despite advances in neuroimaging, there are currently limited available methods enabling noninvasive detection of MPs in vivo. Interestingly, upon activation and subsequent differentiation toward a proinflammatory phenotype MPs undergo metabolic reprogramming that results in increased glycolysis and production of lactate. Hyperpolarized (HP) Read more

Caroline Guglielmetti, Chloé Najac, Alessandro Didonna, Annemie Van der Linden, Sabrina M. Ronen, and Myriam M. Chaumeil

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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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High-Resolution 3D FIB-SEM Image Analysis and Validation of Numerical Simulations of Nanometre-Scale Porous Ceramic with Comparisons to Experimental Results

High-Resolution 3D FIB-SEM Image Analysis and Validation of Numerical Simulations of Nanometre-Scale Porous Ceramic with Comparisons to Experimental Results

The development of focused ion beam-scanning electron microscopy (FIB-SEM) techniques has allowed high-resolution 3D imaging of nanometre-scale porous materials. These systems are of important interest to the oil and gas sector, as well as for the safe long-term storage of carbon and nuclear waste. This work focuses on validating the accurate representation of sample pore space in FIB-SEM-reconstructed volumes and the predicted permeability of these systems from subsequent single-phase flow s... Read more

Department of Chemical Engineering, Qatar Carbonates and Carbon Storage Research Centre, Imperial College London | Department of Applied Mathematics and Theoretical Physics, Cambridge University

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Deep nuclear invaginations are linked to cytoskeletal filaments – integrated bioimaging of epithelial cells in 3D culture

Deep nuclear invaginations are linked to cytoskeletal filaments – integrated bioimaging of epithelial cells in 3D culture

The importance of context in regulation of gene expression is now an accepted principle; yet the mechanism by which the microenvironment communicates with the nucleus and chromatin in healthy tissues is poorly understood. A functional role for nuclear and cytoskeletal architecture is suggested by the phenotypic differences observed between epithelial and mesenchymal cells…

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Danielle M. Jorgens, Jamie L. Inman, Michal Wojcik, Claire Robertson, Hildur Palsdottir, Wen-Ting Tsai, Haina Huang, Alexandre Bruni-Cardoso, Claudia S. López, Mina J. Bissell, Ke Xu, Manfred Auer

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In-situ, time resolved monitoring of uranium in BFS:OPC grout. Part 2: Corrosion in water

In-situ, time resolved monitoring of uranium in BFS:OPC grout. Part 2: Corrosion in water

To reflect potential conditions in a geological disposal facility, uranium was encapsulated in grout and submersed in de-ionised water for time periods between 2–47 weeks. Synchrotron X-ray Powder Diffraction and X-ray Tomography were used to identify the dominant corrosion products and measure their dimensions. Uranium dioxide was observed as the dominant corrosion product and time dependent thickness measurements were used to calculate oxidation rates. The effectiveness of physical and ch... Read more

C. A. Stitt, C. Paraskevoulakos, A. Banos, N. J. Harker, K. R. Hallam, H. Pullin, A. Davenport, S. Street, T. B. Scott

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Application of nuclear volume measurements to comprehend the cell cycle in root-knot nematode-induced giant cells

Application of nuclear volume measurements to comprehend the cell cycle in root-knot nematode-induced giant cells

Root-knot nematodes induce galls that contain giant-feeding cells harboring multiple enlarged nuclei within the roots of host plants. It is recognized that the cell cycle plays an essential role in the set-up of a peculiar nuclear organization that seemingly steers nematode feeding site induction and development. Functional studies of a large set of cell cycle genes in transgenic lines of the model host Arabidopsis thaliana have contributed to better understand the role of the cell cycle comp... Read more

Antonino de Souza Junior José Dijair, Pierre Olivier, Coelho Roberta R., Grossi-de-Sa Maria F., Engler Gilbert, de Almeida Engler Janice / Institut National de la Recherche Agronomique, Université Côte d’Azur, Centre National de la Recherche Scientifique, Institut Sophia Agrobiotech, Sophia-Antipolis, France

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Cytoplasmic and Nuclear Retained DMPK mRNAs Are Targets for RNA Interference in Myotonic Dystrophy Cells

Cytoplasmic and Nuclear Retained DMPK mRNAs Are Targets for RNA Interference in Myotonic Dystrophy Cells

This paper demonstrates for the first time down-regulation of the endogenous nuclear retained mutant DMPK mRNAs targeted with lentivirus-delivered short hairpin RNAs (shRNAs). This nuclear RNAi(-like) phenomenon was not observed when synthetic siRNAs were delivered by cationic lipids, suggesting either a link between processing of the shRNA and nuclear import or a separate pathway for processing shRNAs in the nuclei.

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Marc-André Langlois,  Christelle Boniface,  Gang Wang,  Jessica Alluin, Paul M. Salvaterra,  Jack Puymirat,  John J. Rossi, Nan Sook Lee

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A multi-scale correlative investigation of ductile fracture

A multi-scale correlative investigation of ductile fracture

The use of novel multi-scale correlative methods, which involve the coordinated characterization of matter across a range of length scales, are becoming of increasing value to materials scientists. Here, we describe for the first time how a multi-scale correlative approach can be used to investigate the nature of ductile fracture in metals. Specimens of a nuclear pressure vessel steel, SA508 Grade 3, are examined following ductile fracture using medium and high-resolution 3D X-ray computed to... Read more

School of Materials, University of Manchester; National Nuclear Laboratory; BAM Federal Institute for Materials Research and Testing; Thermo Fischer Scientific

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