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 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.
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
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
Computational fluid dynamics with imaging of cleared tissue and of in vivo perfusion predicts drug uptake and treatment responses in tumours
Understanding the uptake of a drug by diseased tissue, and the drug’s subsequent spatiotemporal distribution, are central factors in the development of effective targeted therapies. However, the interaction between the pathophysiology of diseased tissue and individual therapeutic agents can be complex, and can vary across tissue types and across subjects. Here, we show that the combination of mathematical modelling, high-resolution optical imaging of intact and optically cleared tumour tiss... Read more
Angela d’Esposito, Paul W. Sweeney, Morium Ali, Magdy Saleh, Rajiv Ramasawmy, Thomas A. Roberts, Giulia Agliardi, Adrien Desjardins, Mark F. Lythgoe, R. Barbara Pedley, Rebecca Shipley and Simon Walker-Samuel
Step-by-step guide to post-acquisition correlation of confocal and FIB/SEM volumes using Amira software
In recent years new methodologies and workflow pipelines for acquiring correlated fluorescence microscopy and volume electron microscopy datasets have been extensively described and made accessible to users of different levels. Post-acquisition image processing, and particularly correlation of the optical and electron data in a single integrated three-dimensional framework can be key for extracting valuable information, especially when imaging large sample volumes such as whole cells or tissu... Read more
Comparative Morphology of the Internal Nasal Skeleton of Adult Marsupials Based on X-ray Computed Tomography
The internal skeleton of the nasal cavity is sporadically and often incompletely described for many marsupial species and mammals in general. Here, I provide an anatomical survey of the ethmoid in the skulls of adult marsupials based on examination of computed tomography (CT) imagery of 29 taxa representing all the major extant groups of marsupials. (…) I compared ecological data with the number of ecto- and endoturbinals as a preliminary test to determine whether some of the interspec... Read more
Thomas E. Macrini
A multianalytic investigation of weapon-related injuries in a Late Antiquity necropolis, Mutina, Italy
Human skeletal remains from archaeological contexts occasionally present signs of traumatic injuries from weapons, revealing, for example, the degree of interpersonal violence, the type of weapon and the sequence of events of a specific historical context.
Traumatic lesions are generally analyzed using macroscopic and microscopic methods, which are not necessarily integrated in the same study. In this study, we employed a multi-analytical approach to determine i... Read more
Antonino Vazzana, Lucia Martina Scalise, Mirko Traversari, Carla Figus, Salvatore Andrea Apicella, Laura Buti, Gregorio Oxilia, Rita Sorrentino, Silvia Pellegrini, Chiara Matteucci, Lucio Calcagnile, Raffaele Savigni, Robin N.M.Feeney, Giorgio Gruppioni, Stefano Benazziah
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
VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology
Despite advances in imaging, image-based vascular systems biology has remained challenging because blood vessel data are often available only from a single modality or at a given spatial scale, and cross-modality data are difficult to integrate.
Therefore, there is an exigent need for a multimodality pipeline that enables ex vivo vascular imaging with magnetic resonance imaging, computed tomography and optical microscopy of the same sample, while permitting imaging with complementary c... Read more
Akanksha Bhargava, Benjamin Monteagudo, Priyanka Kushwaha, Janaka Senarathna, Yunke Ren, Ryan C. Riddle , Manisha Aggarwal and Arvind P. Pathak
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.Read more
B.Wang, B.Pan, G.Lubineau
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
Ambient occlusion – A powerful algorithm to segment shell and skeletal intrapores in computed tomography data
During the last decades, X-ray (micro-)computed tomography has gained increasing attention for the description of porous skeletal and shell structures of various organism groups. However, their quantitative analysis is often hampered by the difficulty to discriminate cavities and pores within the object from the surrounding region. Herein, we test the ambient occlusion (AO) algorithm and newly implemented optimisations for the segmentation of cavities (implemented in the software Amira). (... Read more
J. Titschack, D. Baum, K. Matsuyama, K. Boos, C. Farber, W.-A. Kahl, K. Ehrig, D. Meinel, C. Soriano, S.R. Stock
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
Over the rainbow? Micro-CT scanning to non-destructively study Roman and early medieval glass bead manufacture
The usefulness of desktop Micro-CT scanners for the study of archaeological artefacts is demonstrated in a non-destructive study of manufacturing methods of Roman and Early Medieval monochrome and polychrome glass beads. Differences in glass colours show up in these scans as differences in attenuation. The presence and distribution of bubbles and various inclusions (metal, opacifier) are also well visible. Shaft shapes and patterns of bubbles inside the glass make it possible in most cases to... Read more
D.J.M.Ngan-Tillard, D.J.Huisman, F.Corbella, A.Van Nass
A separated vortex ring underlies the flight of the dandelion
Wind-dispersed plants have evolved ingenious ways to lift their seeds. The common dandelion uses a bundle of drag-enhancing bristles (the pappus) that helps to keep their seeds aloft. This passive flight mechanism is highly effective, enabling seed dispersal over formidable distances; however, the physics underpinning pappus-mediated flight remains unresolved. Here we visualized the flow around dandelion seeds, uncovering an extraordinary type of vortex. This vortex is a ring of recirculating... Read more
Cathal Cummins, Madeleine Seale, Alice Macente, Daniele Certini, Enrico Mastropaolo, Ignazio Maria Viola, Naomi Nakayama
X-ray micro-computed tomography for 3D characterization of particle kinematics representing water-induced loess micro-fabric collapse
3D characterisation of the particle kinematics during loess collapse is performed based on X-ray micro-computed tomography.
Particle displacements and rotations associated with the collapse are determined.
The volumetric strain is shown to be significantly heterogeneous at single-particle scale.
The evolution of particle-to-particle contacts is found to be much more complex than previously stated.
An apparatus is specially designed to perf... Read more
B. Yu, W. Fan, J.H. Fan, T.A. Dijkstra, Y.N. Wei, T.T. Wei
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
Improving microstructural quantification in FIB/SEM nanotomography
Advanced nanotomographic analysis is still far from routine, and a number of challenges remain in data acquisition and post-processing. In this work, we present a number of techniques to improve the quality of the acquired data, together with easy-to-implement methods to obtain “advanced” microstructural quantifications. The techniques are applied to a solid oxide fuel cell cathode of interest to the electrochemistry community, but the methodologies are easily adaptable to a wide range of... Read more
Joshua A.Taillon, Christopher Pellegrinelli, Yi-Lin Huang, Eric D.Wachsman, Lourdes G. Salamanca-Riba
Investigation of Hot Pressed Polymer Electrolyte Fuel Cell Assemblies via X-ray Computed Tomography
The hot pressing process for fabricating membrane electrode assemblies (MEAs) has been widely adopted, yet little is known of its effects on the microstructural properties of the different components of the MEA. In particular, the interaction of the electrolyte, electrode and gas diffusion layer (GDL) due to lamination is difficult to probe as conventional imaging techniques cannot access the internal structure of the MEA. Here, a novel approach is used, which combines characterisation of hot... Read more
Q. Meyer, N. Mansor, F. Iacoviello, P.L. Cullen, R. Jervis, D. Finegan, C. Tan, J. Bailey, P. R. Shearing, D. J. L. Brett
Influence of the rheological properties on the steel fibre distribution and orientation in self-compacting concrete
The interest in potential applications produced with self-compacting fibre reinforced concrete continues to grow, but in practice, problems associated with an uneven distribution and orientation of fibres in the concrete structure occur. It is not clear what exactly influences uneven distribution of fibres in selfcompacting concrete (SCC) mixtures, especially during the casting and how different factors influence fibre orientation. The objective of this work was to investigate how rheological... Read more
Elena Jasiuniene, Vaidotas Cicenas, Paulius Grigaliunas, Zymantas Rudzionis, Arunas Aleksandras Navickas
Operative Anatomy of the Human Skull: A Virtual Reality Expedition
Benjamin K Hendricks, MD Akash J Patel, MD Jerome Hartman Mark F Seifert, PhD Aaron Cohen-Gadol, MD, MSc, MBA
Characterization of the bone marrow adipocyte niche with three-dimensional electron microscopy
Unlike white and brown adipose tissues, the bone marrow adipocyte (BMA) exists in a microenvironment containing unique populations of hematopoietic and skeletal cells.
To study this microenvironment at the subcellular level, we performed a three-dimensional analysis of the ultrastructure of the BMA niche with focused ion beam scanning electron microscopy (FIB-SEM). This revealed that BMAs display hallmarks of metabolically active cells including polarized lipid deposits, a dense mitoch... Read more
Hero Robles, SungJae Park, Matthew S. Joens, James A.J. Fitzpatrick, Clarissa S. Craft, Erica L. Scheller