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 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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X-ray computed tomography comparison of individual and parallel assembled commercial lithium iron phosphate batteries at end of life after high rate cycling

X-ray computed tomography comparison of individual and parallel assembled commercial lithium iron phosphate batteries at end of life after high rate cycling

X-ray computed tomography (X-ray CT) across multiple length scales is utilized for the first time to investigate the physical abuse of high C-rate pulsed discharge on cells wired individually and in parallel.. Manufactured lithium iron phosphate cells boasting high rate capability were pulse power tested in both wiring conditions with high discharge currents of 10C for a high number of cycles (up to 1200) until end of life (<80% of initial discharge capacity retained). The parallel ass... Read more

Rachel Carter, Brett Huhman, Corey T. Love, Iryna V. Zenyuk

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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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Four-Dimensional Studies of Morphology Evolution in Lithium–Sulfur Batteries

Four-Dimensional Studies of Morphology Evolution in Lithium–Sulfur Batteries

Lithium sulfur (Li–S) batteries have great potential as a successor to Li-ion batteries, but their commercialization has been complicated by a multitude of issues stemming from their complex multiphase chemistry. In situ X-ray tomography investigations enable direct observations to be made about a battery, providing unprecedented insight into the microstructural evolution of the sulfur cathode and shedding light on the reaction kinetics of the sulfur phase. Here, for the first time, the mor... Read more

Chun Tan, Thomas M. M. Heenan, Ralf F. Ziesche, Sohrab R. Daemi, Jennifer Hack, Maximilian Maier, Shashidhara Marathe, Christoph Rau, Daniel J. L. Brett, Paul R. Shearing

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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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Operando Visualization and Multi-scale Tomography Studies of Dendrite Formation and Dissolution in Zinc Batteries

Operando Visualization and Multi-scale Tomography Studies of Dendrite Formation and Dissolution in Zinc Batteries

Alternative battery technologies are required to meet growing energy demands and address the limitations of present technologies. As such, it is necessary to look beyond lithium-ion batteries. Zinc batteries enable high power density while being sourced from ubiquitous and cost-effective materials. This paper presents, for the first time known to the authors, multi-length scale tomography studies of failure mechanisms in zinc batteries with and without commercial microporous separators. In bo... Read more

Vladimir Yufit, Farid Tariq David S. Eastwood Moshiel Biton Billy Wu Peter D. Lee Nigel P. Brandon

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Nondestructive, longitudinal measurement of collagen scaffold degradation using computed tomography and gold nanoparticles

Nondestructive, longitudinal measurement of collagen scaffold degradation using computed tomography and gold nanoparticles

Biodegradable materials, such as collagen scaffolds, are used extensively in clinical medicine for tissue regeneration and/or as an implantable drug delivery vehicle. However, available methods to study biomaterial degradation are typically invasive, destructive, and/or non-volumetric. Therefore, the objective of this study was to investigate a new method for nondestructive, longitudinal, and volumetric measurement of collagen scaffold degradation. Gold nanoparticles (Au NPs) were covalently ... Read more

Tyler A. Finamore, Tyler E. Curtis, James V. Tedesco, Kathryn Grandfield, Ryan K. Roeder

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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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Metal-organic frameworks tailor the properties of aluminum nanocrystals

Metal-organic frameworks tailor the properties of aluminum nanocrystals

Metal-organic frameworks (MOFs) and metal nanoparticles are two classes of materials that have received considerable recent attention, each for controlling chemical reactivities, albeit in very different ways. Here, we report the growth of MOF shell layers surrounding aluminum nanocrystals (Al NCs), an Earth-abundant metal with energetic, plasmonic, and photocatalytic properties. The MOF shell growth proceeds by means of dissolution-and-growth chemistry that uses the intrinsic surface oxide o... Read more

Hossein Robatjazi, Daniel Weinberg, Dayne F. Swearer, Christian Jacobson, Ming Zhang, Shu Tian, Linan Zhou, Peter Nordlander, Naomi J. Halas

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Aging of a Pt/Al2O3 exhaust gas catalyst monitored by quasi in situ X-ray micro computed tomography

Aging of a Pt/Al2O3 exhaust gas catalyst monitored by quasi in situ X-ray micro computed tomography

Catalyst aging effects were analyzed using X-ray absorption micro-computed tomography in combination with conventional characterization methods on various length scales ranging from nm to μm to gain insight into deactivation mechanisms.

For this purpose, a 4 wt% Pt/Al2O3 model exhaust gas catalyst was coated on a cordierite honeycomb and subjected to sequential thermal aging in static air at 950 °C for 4, 8, 12 and 24 hours. The ag... Read more

Georg Hofmann, Amélie Rochet, Elen Ogel, Maria Casapu, Stephan Ritter, Malte Ogurreck and Jan-Dierk Grunwaldt

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Visualizing the Carbon Binder Phase of Battery Electrodes in Three Dimensions

Visualizing the Carbon Binder Phase of Battery Electrodes in Three Dimensions

This study presents a technique to directly characterize the carbon and binder domain (CBD) in lithium-ion (Li-ion) battery electrodes in three dimensions and use it to determine the effective transport properties of a LiNi0.33Mn0.33Co0.33O2 (NMC) electrode. X-ray nanocomputed tomography (nano-CT) is used to image an electrode composed solely of carbon and binder, whereas focused ion beam–scanning electron microscopy is used to analyze cross-sect... Read more

Sohrab R. Daemi, Chun Tan, Tobias Volkenandt, Samuel J. Cooper, Anna Palacios-Padros, James Cookson, Dan J. L. Brett, and Paul R. Shearing

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Spatially resolved ultrasound diagnostics of Li-ion battery electrodes

Spatially resolved ultrasound diagnostics of Li-ion battery electrodes

The importance of reliable battery diagnostic systems has grown substantially in recent years as a result of the use of high power Li-ion battery packs in an increasingly diverse range of applications. Here, spatially resolved ultrasound acoustic measurements are used to analyse the condition of Li-ion electrodes. Ultrasonic measurements are performed on a commercial mobile phone battery over the full operating voltage window with the lithiation and delithiation of electrodes o... Read more

James B. Robinson, Maximilian Maier , George Alster , Tomos Compton , Dan J. L. Brett and Paul R. Shearing

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Structure of the Ty3/Gypsy retrotransposon capsid and the evolution of retroviruses

Structure of the Ty3/Gypsy retrotransposon capsid and the evolution of retroviruses

Retroviruses evolved from long terminal repeat (LTR) retrotransposons by acquisition of envelope functions, and subsequently reinvaded host genomes. Together, endogenous retroviruses and LTR retrotransposons represent major components of animal, plant, and fungal genomes. Sequences from these elements have been exapted to perform essential host functions, including placental development, synaptic communication, and transcriptional regulation. They encode a Gag polypeptide, the capsid domains ... Read more

Svetlana O. Dodonova, Simone Prinz, Virginia Bilanchone, Suzanne Sandmeyer, and John A. G. Briggs

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Differentiation and Characterization of Excitatory and Inhibitory Synapses by Cryo-electron Tomography and Correlative Microscopy

Differentiation and Characterization of Excitatory and Inhibitory Synapses by Cryo-electron Tomography and Correlative Microscopy

As key functional units in neural circuits, different types of neuronal synapses play distinct roles in brain information processing, learning, and memory. Synaptic abnormalities are believed to underlie various neurological and psychiatric disorders. Here, by combining cryo-electron tomography and cryo-correlative light and electron microscopy, we distinguished intact excitatory and inhibitory synapses of cultured hippocampal neurons, and visualized the in situ 3D organization of ... Read more

Chang-Lu Tao, Yun-Tao Liu, Rong Sun, Bin Zhang, Lei Qi, Sakar Shivakoti, Chong-Li Tian, Peijun Zhang, Pak-Ming Lau, Z. Hong Zhou and Guo-Qiang Bi

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Cerebral Corpora amylacea are dense membranous labyrinths containing structurally preserved cell organelles

Cerebral Corpora amylacea are dense membranous labyrinths containing structurally preserved cell organelles

Corpora amylacea are cell-derived structures that appear physiologically in the aged human brain. While their histological identification is straightforward, their ultrastructural composition and microenvironment at the nanoscale have remained unclear so far, as has their relevance to aging and certain disease states that involve the sequestration of toxic cellular metabolites. Here, we apply correlative serial block-face scanning electron microscopy and transmission electron tomograp... Read more

Paula P. Navarro, Christel Genoud, Daniel Castaño-Díez, Alexandra Graff-Meyer, Amanda J. Lewis, Yvonne de Gier, Matthias E. Lauer, Markus Britschgi, Bernd Bohrmann, Stephan Frank, Jürgen Hench, Gabriel Schweighauser, Annemieke J. M. Rozemuller, Wilma D. J. van de Berg, Henning Stahlberg & Sarah H. Shahmoradian

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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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Determining the bacterial cell biology of planctomycetes

Determining the bacterial cell biology of planctomycetes

Bacteria of the phylum Planctomycetes have been previously reported to possess several features that are typical of eukaryotes, such as cytosolic compartmentalization and endocytosis-like macromolecule uptake. However, recent evidence points towards a Gram-negative cell plan for Planctomycetes, although in-depth experimental analysis has been hampered by insufficient genetic tools…

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Christian Boedeker, Margarete Schüler, Greta Reintjes, Olga Jeske, Muriel C. F. van Teeseling et al.

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Three-dimensional imaging of the intracellular assembly of a functional viral RNA replicase complex

Three-dimensional imaging of the intracellular assembly of a functional viral RNA replicase complex

Positive-strand RNA viruses, which can be devastating pathogens in humans, animals and plants, replicate their genomes on intracellular membranes. Here, we describe the three-dimensional ultrastructural organization of a tombusvirus replicase in yeast, a valuable model for exploring virus–host interactions…

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Isabel Fernández de Castro, José J. Fernández, Daniel Barajas, Peter D. Nagy, Cristina Risco

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Fast and precise targeting of single tumor cells in vivo by multimodal correlative microscopy

Fast and precise targeting of single tumor cells in vivo by multimodal correlative microscopy

Intravital microscopy provides dynamic understanding of multiple cell biological processes, but its limited resolution has so far precluded structural analysis. Because it is difficult to capture rare and transient events, only a few attempts have been made to observe specific developmental and pathological processes in animal models using electron microscopy. The multimodal correlative approach that we propose here combines intravital microscopy, microscopic X-ray computed tomography and thr... Read more

Matthia A. Karreman, Luc Mercier, Nicole L. Schieber, Gergely Solecki, Guillaume Allio, Frank Winkler, Bernhard Ruthensteiner, Jacky G. Goetz, Yannick Schwab

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Chromosome segregation occurs by microtubule pushing in oocytes

Chromosome segregation occurs by microtubule pushing in oocytes

During cell division, spindle microtubules ensure an equal repartition of chromosomes between the two daughter cells. While the kinetochore-dependent mechanisms that drive mitotic chromosome segregation are well understood, in oocytes of most species atypical spindles assembled in absence of centrosomes entail poorly understood mechanisms of chromosome segregation. In particular, the structure(s) responsible for force generation during meiotic chromosome separation in oocytes is unclear. Usin... Read more

Kimberley Laband, Rémi Le Borgne, Frances Edwards, Marine Stefanutti, Julie C. Canman, Jean-Marc Verbavatz, Julien Dumont

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High-resolution structures of HIV-1 Gag cleavage mutants determine structural switch for virus maturation

High-resolution structures of HIV-1 Gag cleavage mutants determine structural switch for virus maturation

HIV-1 maturation occurs via multiple proteolytic cleavages of the Gag polyprotein, causing rearrangement of the virus particle required for infectivity. (…) How individual cleavages contribute to changes in protein structure and interactions, and how the mature, conical capsid forms, are poorly understood. Here, we employed cryoelectron tomography to determine morphology and high-resolution CA lattice structures for HIV1 derivatives in which Gag cleavage sites are mutated. These analyse... Read more

Simone Mattei, Aaron Tan, Barbel Glass, Barbara Muller, Hans-Georg Krausslich, and John A. G. Briggs

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