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.
Focused-ion beam-scanning electron microscopic (FIB-SEM) tomography enables easier acquisition of a series of ultrastructural, sectional images directly from resin-embedded biological samples. In this study, to clarify the three-dimensional (3D) architecture of glomerular endothelial cells (GEnCs) in adult rats, we manually extracted GEnCs from serial FIB-SEM images and reconstructed them on an Amira reconstruction software. The luminal and basal surface structures were clearly visualized in ... Read more
Yuto Kawasaki, Yasue Hosoyamada, Takayuki Miyaki, Junji Yamaguchi, Soichiro Kakuta, Tatsuo Sakai, and Koichiro Ichimura
The liver contains a variety of vessels and participates in miscellaneous physiological functions. While past studies generally focused on certain hepatic vessels, we simultaneously obtained all the vessels and cytoarchitectural information of the intact mouse liver lobe at single-cell resolution. […] providing a technology roadmap for studying the fine hepatic vascular structures and their spatial relationship, which will help research into liver diseases and evaluation of medical effi... Read more
Qi Zhang, Anan Li, Siqi Chen, Jing Yuan, Tao Jiang, Xiangning Li, Qingming Luo,Zhao Feng & Hui Gon
Our study placed emphasis on solving problems in processing high-throughput bright field images and made attempt in developing a method for the extraction and reconstruction of multiple structures. This will facilitate a better understanding of the cerebral anatomical features under the pathological state of AD and shows extensive application prospect in drug efficacy assessment from brain-wide level.
Simultaneously visualizing Amyloid-β (Aβ) plaque with its surrounding brain structu... Read more
Xianzhen Yin, Xiaochuan Zhang, Jingjing Zhang, Weicheng Yang, Xian Sun, Haiyan Zhang, Zhaobing Gao, Hualiang Jiang
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
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
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
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
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
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
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
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
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
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
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
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
Glass foams are attractive thermal insulation materials, thus, the thermal conductivity (λ) is crucial for their insulating performance. Understanding the foaming process is critical for process optimization. Here, we applied high-speed synchrotron X-ray tomography to investigate the change in pore structure during the foaming process, quantifying the foam structures and porosity dynamically. The results can provide guidance for the manufacturing of glass foams. The 3D pore structures were a... Read more
Martin B. Østergaard, Manlin Zhang, Xiaomei Shen, Rasmus R. Petersen, Jakob König, Peter D. Lee, Yuanzheng Yue, Biao Cai
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
Cortical bone is permeated by a system of pores, occupied by the blood supply and osteocytes. With ageing, bone mass reduction and disruption of the microstructure are associated with reduced vascular supply. Insight into the regulation of the blood supply to the bone could enhance the understanding of bone strength determinants and fracture healing. Using synchrotron radiation-based computed tomography, the distribution of vascular canals and osteocyte lacunae was assessed in murine cortica... Read more
J.A. Núñez; A. Goring; B. Javaheri; H. Razi; D. Gomez-Nicola; E. Hesse; A.A. Pitsillides; P.J. Thurner; P. Schneider; E. Clarkin
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
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
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