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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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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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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Distribution of Serotonin-Immunoreactive Neurons in the Brain and Gnathal Ganglion of Caterpillar Helicoverpa armigera

Distribution of Serotonin-Immunoreactive Neurons in the Brain and Gnathal Ganglion of Caterpillar Helicoverpa armigera

Serotonin (5-hydroxytryptamine, 5-HT) is an important biogenic amine that acts as a neural circuit modulator. It is widespread in the central nervous system of insects. However, little is known about the distribution of serotonin in the nervous system of the cotton bollworm Helicoverpa armigera. In the present study, we performed immunohistochemical experiments with anti-serotonin serum to examine the distribution of serotonin in the central nervous system of H. armigera larv... Read more

Qing-Bo Tang, Wei-Wei Song, Ya-Jun Chang, Gui-Ying Xie, Wen-Bo Chen* and Xin-Cheng Zhao

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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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An adult brain atlas reveals broad neuroanatomical changes in independently evolved populations of Mexican cavefish

An adult brain atlas reveals broad neuroanatomical changes in independently evolved populations of Mexican cavefish

A shift in environmental conditions impacts the evolution of complex developmental and behavioral traits. The Mexican cavefish, Astyanax mexicanus, is a powerful model for examining the evolution of development, physiology, and behavior because multiple cavefish populations can be compared to an extant and ancestral-like surface population of the same species. Many behaviors have diverged in cave populations of A. mexicanus, and previous studies have shown that cavefish ha... Read more

Cody Loomis, View ORCID ProfileRobert Peuß, James Jaggard, Yongfu Wang, Sean McKinney, Stephen Raftopoulos, Austin Raftopoulos, Daniel Whu, Matthew Green, Suzanne E. McGaugh, Nicolas Rohner, Alex C. Keene, Erik R. Duboue

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Variation of 3D outer and inner crown morphology in modern human mandibular premolars

Variation of 3D outer and inner crown morphology in modern human mandibular premolars

This study explores the outer and inner crown of lower third and fourth premolars (P3, P4) by analyzing the morphological variation among diverse modern human groups.

We studied three‐dimensional models of the outer enamel surface and the enamel–dentine junction (EDJ) from μCT datasets of 77 recent humans using both an assessment of seven nonmetric traits and a standard geometric morphometric (GM) analysis. For the latter, the dental crown was represented by ... Read more

Viktoria A. Krenn, Cinzia Fornai, Lisa Wurm, Fred L. Bookstein, Martin Haeusler, Gerhard W. Weber

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Characterization of 3D fracture evolution in concrete using in-situ X-Ray Computed Tomography testing and Digital Volume Correlation

Characterization of 3D fracture evolution in concrete using in-situ X-Ray Computed Tomography testing and Digital Volume Correlation

X-ray Computed Tomography (XCT) is a powerful technology that can accurately image the internal structures of composite and heterogeneous materials in three-dimensions (3D). In this study, in-situ micro XCT tests of concrete specimens under progressive compressive loading are carried out. The aim of the observations is to gain a better understanding of 3D fracture and failure mechanisms at the meso-scale. To characterise the fracture evolution as the deformation increases, two methods are use... Read more

College of Civil Engineering and Architecture, Zhejiang University | School of Mechanical, Aerospace and Civil Engineering, the University of Manchester | Manchester X-ray Imaging Facility | Oxford Martin School and Department of Materials

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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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Cognition based bTBI mechanistic criteria; a tool for preventive and therapeutic innovations

Cognition based bTBI mechanistic criteria; a tool for preventive and therapeutic innovations

Blast-induced traumatic brain injury has been associated with neurodegenerative and neuropsychiatric disorders. To date, although damage due to oxidative stress appears to be important, the specific mechanistic causes of such disorders remain elusive. Here, to determine the mechanical variables governing the tissue damage eventually cascading into cognitive deficits, we performed a study on the mechanics of rat brain under blast conditions. To this end, experiments were carried out to analyse... Read more

Daniel Garcia-Gonzalez, Nicholas S. Race, Natalie L. Voets, Damian R. Jenkins, Stamatios N. Sotiropoulos, Glen Acosta, Marcela Cruz-Haces, Jonathan Tang, Riyi Shi & Antoine Jérusalem

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Three-Dimensional In Situ XCT Characterisation and FE Modelling of Cracking in Concrete

Three-Dimensional In Situ XCT Characterisation and FE Modelling of Cracking in Concrete

An improved understanding of 3D cracking in concrete can be achieved by multiscale experiments and numerical modelling based on realistic microstructures, for the development of materials with higher strength, durability, and fracture resistance.

Three-dimensional (3D) characterisation and modelling of cracking in concrete have been always of great importance and interest in civil engineering. In this study, an in situ microscale X-ray computed tomography (XCT) test was carried out to ... Read more

Wenyuan Ren, Zhenjun Yang, Rajneesh Sharma, Samuel A. McDonald, Paul M. Mummery

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Three-dimensional image based modelling of transport parameters in lithium–sulfur batteries

Three-dimensional image based modelling of transport parameters in lithium–sulfur batteries

An elemental sulfur electrode was imaged with X-ray micro and nano computed tomography and segmented into its constituent phases. Morphological parameters including phase fractions and pore and particle size distributions were calculated directly from labelled image data, and flux based simulations were performed to determine the effective molecular diffusivity of the pore phase and electrical conductivity of the conductive carbon and binder phase, D... Read more

Chun Tan, Matthew D. R. Kok , Sohrab R. Daemi , Daniel J. L. Brett and Paul R. Shearing

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Multiscale tomographic analysis of the thermal failure of Na-Ion batteries

Multiscale tomographic analysis of the thermal failure of Na-Ion batteries

In recent years, the ability to examine the processes that cause the catastrophic failure of batteries as a result of thermal runaway has improved substantially. In this work, the effect of thermal runaway on the microstructure of the electrodes of a Na-ion battery is examined using X-ray computed tomography for the first time. The thermal failure induced via accelerating rate calorimetry enabled the examination of failed electrodes, which were subsequently compared with fresh s... Read more

Robinson, J. B., Heenan, T. M. M., Jervis, J. R., Tan, C., Kendrick, E., Brett, D. J. L., & Shearing, P. R.

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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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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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Porous Metal–Organic Frameworks for Enhanced Performance Silicon Anodes in Lithium-Ion Batteries

Porous Metal–Organic Frameworks for Enhanced Performance Silicon Anodes in Lithium-Ion Batteries

Maintaining the physical integrity of electrode microstructures in Li-ion batteries is critical to significantly extend their cycle life. This is especially important for high-capacity anode materials such as silicon, whose operational volume expansion exerts huge internal stress within the anode, resulting in electrode destruction and capacity fade. In this study, we demonstrate that by incorporating metal–organic frameworks (MOFs) with carboxylate organic linkers into Si-based anodes, a s... Read more

Romeo Malik, Melanie. J. Loveridge, Luke J. Williams, Qianye Huang, Geoff West, Paul R. Shearing, Rohit Bhagat, Richard I. Walton

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Microstructural evolution and deformation behavior of Al-Cu alloys: A Transmission X-ray Microscopy (TXM) and micropillar compression study

Microstructural evolution and deformation behavior of Al-Cu alloys: A Transmission X-ray Microscopy (TXM) and micropillar compression study

A unique approach to correlating an evolving 3D microstructure in an Al-Cu alloyand its micro-scale mechanical properties has been introduced. Using these nanoscale three-dimensional microstructures derived from Transmission X-rayMicroscopy (TXM), individual contributions from different strengthening mechanisms were quantified. The spatial distribution and morphology of the individual θ′ and θ phases were seen to play an important role in influencing dislocation storage. Uniaxi... Read more

C. Shashank Kaira, Christopher Kantzos, Jason J. Williams, Vincent De Andrade, Francesco De Carlo, Nikhilesh Chawlaa

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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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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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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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Novel Sulfolobus Virus with an Exceptional Capsid Architecture

Novel Sulfolobus Virus with an Exceptional Capsid Architecture

A novel archaeal virus, denoted Sulfolobus ellipsoid virus 1 (SEV1), was isolated from an acidic hot spring in Costa Rica. The morphologically unique virion of SEV1 contains a protein capsid with 16 regularly spaced striations and an 11-nm-thick envelope. The capsid exhibits an unusual architecture in which the viral DNA, probably in the form of a nucleoprotein filament, wraps around the longitudinal axis of the virion in... Read more

Haina Wang, Zhenqian Guo, Hongli Feng, Yufei Chen, Xiuqiang Chen, Zhimeng Li, Walter Hernández-Ascencio, Xin Dai, Zhenfeng Zhang, Xiaowei Zheng, Marielos Mora-López, Yu Fu, Chuanlun Zhang, Ping Zhu, Li Huang

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3D visualization and deep-learning reveal complex parasite networks in behaviorally manipulated ants

3D visualization and deep-learning reveal complex parasite networks in behaviorally manipulated ants

Microbial parasites may behave collectively to manipulate their host’s behavior. We examine adaptations of a microbial parasite in its natural environment: the body of its coevolved and manipulated host.

Electron microscopy and 3D reconstructions of host and parasite tissues reveal that this fungus invades muscle fibers throughout the ant’s body but leaves the brain intact, and that the fungal cells connect to form extensive networks.

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Maridel A. Fredericksena, Yizhe Zhangb, Missy L. Hazenc, Raquel G. Loretoa,d, Colleen A. Mangoldd,e, Danny Z. Chenb, and David P. Hughes, Department of Entomology, Pennsylvania State University

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