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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The Ebola virus VP40 matrix layer undergoes endosomal disassembly essential for membrane fusion

The Ebola virus VP40 matrix layer undergoes endosomal disassembly essential for membrane fusion

Ebola viruses (EBOVs) assemble into filamentous virions, whose shape and stability are determined by the matrix viral protein 40 (VP40). Virus entry into host cells occurs via membrane fusion in late endosomes; however, the mechanism of how the remarkably long virions undergo uncoating, including virion disassembly and nucleocapsid release into the cytosol, remains unknown. Here, we investigate the structural architecture of EBOVs entering host cells and discover that the VP40 matrix disassem... Read more

Sophie L Winter, Gonen Golani, Fabio Lolicato, Melina Vallbracht, Keerthihan Thiyagarajah, Samy Sid Ahmed, Christian Lüchtenborg, Oliver T Fackler, Britta Brügger, Thomas Hoenen, Walter Nickel Ulrich S Schwarz, Petr Chlanda

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Electrochemical recovery of lithium-ion battery materials from molten salts by microstructural characterization using X-ray imaging

Electrochemical recovery of lithium-ion battery materials from molten salts by microstructural characterization using X-ray imaging

Recycling spent lithium-ion batteries (LiBs) guarantees the conservation of important metal resources by reducing demands on raw supply and offsetting the energy and environmental costs associated with its manufacture. Employing a molten salt as a solvent for extraction affords a much greener and simpler route to metal recovery by electrochemical means. The current mechanistic understanding of the electrochemical recovery of metals in molten salts needs to be improved for the process to be op... Read more

Mateen Mirza, Wenjia Du, Lara Rasha, Steven Wilcock, Arfon H. Jones, Paul R. Shearing, Dan J.L. Brett

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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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Three-dimensional grain mapping of open-cell metallic foam by integrating synthetic data with experimental data from high-energy X-ray diffraction microscopy

Three-dimensional grain mapping of open-cell metallic foam by integrating synthetic data with experimental data from high-energy X-ray diffraction microscopy

The complex mechanical response of open-cell foams depends strongly on the hierarchy of length scales inherent in them, from engineering-part scale to the ligament scale through the grain scale down to the crystal-lattice scale. A first step toward understanding and predicting the coordinated mechanical response across le... Read more

Jayden C. Plumb, Jonathan F. Lind, Joseph C. Tucker, Ron Kelley, Ashley D. Spear

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Multi-modal plasma focused ion beam serial section tomography of an organic paint coating

Multi-modal plasma focused ion beam serial section tomography of an organic paint coating

Pigment distributions have a critical role in the corrosion protection properties of organic paint coatings, but they are difficult to image in 3D over statistically significant volumes and at sufficiently high spatial resolutions required for detailed analysis. Here we report, for the first time, large volume analytical serial sectioning tomography of an organic composite coating using a xenon Plasma Focused Ion Beam (PFIB) combined with secondary electron imaging, energy dispersive X-ray (E... Read more

Zhong Xiangli, M. Grace Burke, Philip J. Withers, Zhang Xun, Zhou Xiaorong, Timothy L. Burnett, Liu Yanwen, Stuart B. Lyon, Simon R.Gibbon

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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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In Situ Synthesized La0.6Sr0.4Co0.2Fe0.8O3−δ–Gd0.1Ce0.9O1.95 Nanocomposite Cathodes via a Modified Sol–Gel Process for Intermediate Temperature Solid Oxide Fuel Cells

In Situ Synthesized La0.6Sr0.4Co0.2Fe0.8O3−δ–Gd0.1Ce0.9O1.95 Nanocomposite Cathodes via a Modified Sol–Gel Process for Intermediate Temperature Solid Oxide Fuel Cells

Composite cathodes comprising nanoscale
powders are expected to impart with high specific surface
area and triple phase boundary (TPB) density, which will lead
to better performance.

However, uniformly mixing nanosized heterophase powders remains a challenge due to their high surface energy and thus ease with which they agglomerate into their individual phases during the mixing and sintering
processes. In this study, we successfully synthesized La0.6Sr0.4Co0.2Fe... Read more

Dong Woo Joh, Areum Cha, Jeong Hwa Park, Kyeong Joon Kim, Kyung Taek Bae, Doyeub Kim, Young Ki Choi, Hyegsoon An, Ji Su Shin, Kyung Joong Yoon, and Kang Taek Lee

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Preclinical Evaluation of 203/212Pb-Labeled Low-Molecular-Weight Compounds for Targeted Radiopharmaceutical Therapy of Prostate Cancer

Preclinical Evaluation of 203/212Pb-Labeled Low-Molecular-Weight Compounds for Targeted Radiopharmaceutical Therapy of Prostate Cancer

Targeted radiopharmaceutical therapy (TRT) using α-particle radiation is a promising approach for treating both large and micrometastatic lesions. Researchers developed prostate-specific membrane antigen (PSMA)–targeted low-molecular-weight agents for 212Pb-based TRT of patients with prostate cancer (PC) by evaluating the matching γ-emitting surrogate.

Targeted radiopharmaceutical therapy using α-particles (α-TRTs), which cause deposition of ionizing radiation of high-linear-ener... Read more

Sangeeta Ray Banerjee, Il Minn, Vivek Kumar, Anders Josefsson, Ala Lisok, Mary Brummet, Jian Chen, Ana P. Kiess, Kwamena Baidoo, Cory Brayton, Ronnie C. Mease, Martin Brechbiel, George Sgouros, Robert F. Hobbs, and Martin G. Pomper

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Visual research filler network structure in polymer composites and its structure-activity relationship by fluorescent labeling and LSCM

Visual research filler network structure in polymer composites and its structure-activity relationship by fluorescent labeling and LSCM

For organic-inorganic composite materials, the spatial dispersion of inorganic fillers in the organic matrix is of great significance for designing and manufacturing high-performance composite materials. To improve the understanding of the micro-physical mechanism of the filler-reinforced polymer matrix, we studied the relationship between filler network structure and macro-mechanical properties of silicone rubber by using fluorescent labeling technology and three-dimensional (3D) visualizati... Read more

Shangjun Zeng, Ming Kang, Kexu Chen, Rong Sun, Ai Lu, Guanjun Changa

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Multi-method characterization approach to facilitate a strategy to design mechanical and electrical properties of sintered copper

Multi-method characterization approach to facilitate a strategy to design mechanical and electrical properties of sintered copper

Porous materials have attracted great attention for various applications, e.g., catalysis, novel materials, energy related topics, acoustics, microelectronics, actuator, bioengineering and biomimetic. Recently, porous materials have gained interest as interconnect materials for power semiconductor device.

The trend in the semiconductor industry goes towards eco-friendliness and higher energy efficiency. Semiconductor compound materials, such as silicon carbide (SiC) or gallium nitride... Read more

A.Wijaya, B.Eichinger, F.F.Chamasemani, B.Sartory, R.Hammer, V.Maier-Kiener, D.Kiener, M.Mischitz, R.Brunner

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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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In situ compression and X-ray computed tomography of flow battery electrodes

In situ compression and X-ray computed tomography of flow battery electrodes

Redox flow batteries offer a potential solution to an increase in renewable energy generation on the grid by offering long-term, large-scale storage and regulation of power. However, they are currently underutilised due to cost and performance issues, many of which are linked to the microstructure of the porous carbon electrodes used. Here, for the first time, we offer a detailed study of the in situ effects of compression on a commercially available carbon felt electrode. Visualisation ... Read more

Rhodri Jervis , Matt D.R. Kok , Tobias P. Neville , Quentin Meyer , Leon D. Brown , Francesco Iacoviello , Jeff T. Gostick , Dan J.L. Brett , Paul R. Shearing

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Three-dimensional thermal stress analysis of the re-oxidized Ni-YSZ anode functional layer in solid oxide fuel cells

Three-dimensional thermal stress analysis of the re-oxidized Ni-YSZ anode functional layer in solid oxide fuel cells

Nickel-yttria-stabilized zirconia (Ni-YSZ) cermet is widely used as an anode material in solid oxide fuel cells (SOFCs); however, Ni re-oxidation causes critical problems due to volume expansion, which causes high thermal stress. We fabricated a Ni-YSZ anode functional layer (AFL), which is an essential component in high-performance SOFCs, and re-oxidized it to investigate the related three-dimensional (3D) microstructural and thermo-mechanical effects. A 3D model of the re-oxidized AFL ... Read more

Jun Woo Kim, Kiho Bae, Hyun Joong Kim, Ji-won Son, Namkeun Kim, Stefan Stenfelt, Fritz B. Prinz, Joon Hyung Shim

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A three-dimensional heterogeneity analysis of electrochemical energy conversion in SOFC anodes using electron nanotomography and mathematical modeling

A three-dimensional heterogeneity analysis of electrochemical energy conversion in SOFC anodes using electron nanotomography and mathematical modeling

In this paper a fully three dimensional, multiphase, micro-scale solid oxide fuel cellanode transport phenomena numerical model is proposed and verified. The Butler-Volmer model was combined with empirical relations for conductivity and diffusivity – notably the Fuller-Shetler-Giddings equation, and the Fickian modelfor transport of gas reagents. FIB-SEM tomography of a commercial SOFC stack anode was performed and the resulting images were processed to acquire input data. ... Read more

Tomasz A. Prokop, Katarzyna Berent, Hiroshi Iwai, Janusz S.Szmyd, Grzegorz Brus

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Enhanced Water Management of Polymer Electrolyte Fuel Cells with Additive-Containing Microporous Layers.

Enhanced Water Management of Polymer Electrolyte Fuel Cells with Additive-Containing Microporous Layers.

This work describes the performance improvement of a polymer electrolyte fuel cell with a novel class of microporous layers (MPLs) that incorporates hydrophilic additives: one with 30 μm aluminosilicate fibers and another with multiwalled carbon nanotubes with a domain size of 5 μm. Higher current densities at low potentials were observed for cells with the additive-containing MPLs compared to a baseline cell with a conventional MPL, which correlate with improvements in water management. Th... Read more

Dusan Spernjak, Rangachary Mukundan, Rodney L. Borup, Liam Connolly, Benjamin Zackin, Vincent De Andrade, Michael Wojcik, Dilworth Y. Parkinson, David Jacobson, Daniel Seth Hussey, Karren L More, Thomas Chan, Adam Z Weber, and Iryna V. Zenyuk

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High performance anode with dendritic porous structure for low temperature solid oxide fuel cells

High performance anode with dendritic porous structure for low temperature solid oxide fuel cells

A dendritic porous supported microstructure simultaneously creates small pore size and broad gas diffusion pathways in a solid oxide fuel cell anode membrane. This microstructure also achieves pore sizes that reduce with increasing depth within the membrane without increasing the structure tortuosity. Such a microstructure supplies high triple phase boundary density, fast gas diffusion and low polarization resistance. Here we characterise the performance of a porous anode with such a dendriti... Read more

Xin Shao, William D.A. Rickard, Dehua Dong, Huu Dang , Martin Saunders, Aaron Dodd, Gordon Parkinson, Chun-Zhu Li

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Cryo-STEM mapping of solid–liquid interfaces and dendrites in lithium-metal batteries

Cryo-STEM mapping of solid–liquid interfaces and dendrites in lithium-metal batteries

Solid–liquid interfaces are important in a range of chemical, physical and biological processes but are often not fully understood owing to the lack of high-resolution characterization methods that are compatible with both solid and liquid components. For example, the related processes of dendritic deposition of lithium metal and the formation of solid–electrolyte interphase layers are known to be key determinants of battery safety and performance in high-energy-density lithium-metal bat... Read more

Michael J. Zachman, Zhengyuan Tu, Snehashis Choudhury, Lynden A. Archer & Lena F. Kourkoutis

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A numerical analysis of unsteady transport phenomena in a Direct Internal Reforming Solid Oxide Fuel Cell

A numerical analysis of unsteady transport phenomena in a Direct Internal Reforming Solid Oxide Fuel Cell

Growing popularity and rapid development of Solid Oxide Fuel Cells (SOFCs) stem for their potential to become a gamechanger in the field of clean power generation technologies.

In this paper, a transient microstructure-oriented numerical simulation of a planar Direct Internal Reforming Solid Oxide Fuel Cell (DIR-SOFC) is delivered. The performance criteria in a direct steam reforming for a fuel starvation scenario are analyzed in order to optimize the underlying process. The proposed t... Read more

Maciej Chalusiak, Michal Wrobel, Marcin Mozdzierz, Katarzyna Berent, Janusz S. Szmyd, Shinji Kimijima, Grzegorz Brus

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4D imaging of polymer electrolyte membrane fuel cell catalyst layers by soft X-ray spectro-tomography

4D imaging of polymer electrolyte membrane fuel cell catalyst layers by soft X-ray spectro-tomography

4D imaging – the three-dimensional distributions of chemical species determined using multi-energy X-ray tomography – of cathode catalyst layers of polymer electrolyte membrane fuel cells (PEM-FC) has been measured by scanning transmission x-ray microscopy (STXM) spectro-tomography at the C 1s and F 1s edges. In order to monitor the effects of radiation damage on the composition and 3D structure of the perfluorosulfonic acid (PFSA) ionomer, the same volume was measu... Read more

Juan Wu, Lis G.A.Melo, Xiaohui Zhu, Marcia M.West, Viatcheslav Berejnov, Darija Susac, Juergen Stumper, Adam P.Hitchcock

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Mesoscale characterization of local property distributions in heterogeneous electrodes

Mesoscale characterization of local property distributions in heterogeneous electrodes

The performance of electrochemical devices depends on the three-dimensional (3D) distributions of microstructural features in their electrodes. Several mature methods exist to characterize 3D microstructures over the microscale (tens of microns), which are useful in understanding homogeneous electrodes. However, methods that capture mesoscale (hundreds of microns) volumes at appropriate resolution (tens of nm) are lacking, though they are needed to understand more common, less ideal electrode... Read more

Tim Hsu, William K. Epting, Rubayyat Mahbub, Noel T. Nuhfer, Sudip Bhattachary, Yinkai Lei, Herbert M. Miller, Paul R. Ohodnicki, Kirk R. Gerdes, Harry W. Abernathy, Gregory A. Hackett, Anthony D. Rollett, Marc De Graef, Shawn Litster, Paul A. Salvador

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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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