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.
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Pulmonary diseases, such as chronic obstructive pulmonary diseases, lower respiratory infections, and lung cancer are listed in the top ten causes of deaths globally with more than 10 million mortality per year. Apart from oral administration, the Dry Powder Inhalation (DPI) for pulmonary administration provides an important alternative route for targeted treatment of these pulmonary diseases. […] Furthermore, there is a growing demand on und... Read more
Xian Sun, Xiaochuan Zhang, Xiaohong Ren, Hongyu Sun, Li Wu, Caifen Wang, Xiaohui Ye, Peter York, Zhaobing Gao, Hualiang Jiang, Jiwen Zhang, Xianzhen Yin
In this work, we studied mitochondria-rER contacts in vivo by serial section electron tomography (SSET) and 3D reconstruction analysis of cryo-fixed mouse tissue samples. We characterized this inter-organelle association as mitochondria tightly wrapped by sheets of curved rER (wrappER). Further, we used multi-omics and genetic approaches to obtain evidence that the wrappER is a distinct intracellular compartment and demonstrate the importance of wrappER-mitochondria contacts for v... Read more
Irene Anastasia, Nicolò Ilacqua, Andrea Raimondi, Philippe Lemieux, Rana Ghandehari-Alavijeh, Guilhem Faure, Sergei L. Mekhedov, Kevin J. Williams, Federico Caicci, Giorgio Valle, Marta Giacomello, Ariel D. Quiroga, Richard Lehner, Michael J. Miksis, Katalin Toth, Thomas Q. de Aguiar Vallim, Eugene V. Koonin, Luca Scorrano, Luca Pellegrini
Actin waves are dynamic supramolecular structures involved in cell migration, cytokinesis, adhesion, and neurogenesis. Although wave-like propagation of actin networks is a widespread phenomenon, the actin architecture underlying wave propagation remained unknown. In situ cryo-electron tomography of Dictyostelium cells unveils the wave architecture and provides evidence for wave progression by de novo actin nucleation. Subtomogram averaging reveals the structu... Read more
Marion Jasnin, Florian Beck, Mary Ecke, Yoshiyuki Fukuda, Antonio Martinez-Sanchez, Wolfgang Baumeister, Günther Gerisch
Lithium ion battery failure occurs across multiple length scales. In this work, the properties of thermal failure and its effects on electrode materials were investigated in a commercial battery using a combination of accelerating rate calorimetry (ARC) and multi-length scale X-ray computed tomography (CT). ARC measured the heat dissipated from the cell during thermal runaway and enabled the identification of key thermal failure characteristics such as onset temperature and the rate of heat g... Read more
Drasti Patel, James B. Robinson, Sarah Ball, Daniel J. L. Brett and Paul R. Shearing
High market demands related to material quality and properties strongly influence redesigning of common safety loaded aluminum alloy castings. The quality of aluminum components and associated obtained mechanical properties are strongly dependent on the casting process and parameters, as well as on the chemical composition. Therefore, the redesigning of chemical composition of high-strength aluminum alloys becomes significant for safety critical structural components in automotive industry.Read more
Davor Stanić, Zdenka Zovko Brodarac, Letian Li
Recent studies have identified gold nanoparticles in ores in a range of deposit types, but little is known about their formation processes. In this contribution, gold-bearing magnetite from the well-documented, world-class Beiya Au deposit, China, was investigated in terms of microstructure and crystallography at the nanoscale. We present the first three-dimensional (3D) focused ion beam/scanning electron microscopy (FIB/SEM) tomography of the distribution of gold nanoparticles in nanopores i... Read more
Haoyang Zhou, Richard Wirth, Sarah A. Gleeson, Anja Schreiber, Sathish Mayanna
The Asian citrus psyllid (ACP), Diaphorina citri, is a harmful pest of citrus trees that transmits Candidatus Liberibacter spp. which causes Huanglongbing (HLB) (citrus greening disease); this is considered to be the most serious bacterial disease of citrus plants.
Here we detail an anatomical study of the external and internal anatomy (excluding the reproductive system) using micro-computed tomography (micro-CT). This is the first complete 3D micro-CT reconstruction o... Read more
Javier Alba-Tercedor, Wayne B. Hunter & Ignacio Alba-Alejandre
Cell-to-cell contact is essential for communication and development of multicellular organisms. A prerequisite is the passage through membranes. That way, molecular exchange and information flow is regulated via hormones, membrane proteins and pores.
In plants, the rigid cell walls prevent large membrane contact areas between protoplasts. Only plasmodesmata, minute channels between adjacent cells, form direct connections. Often, molecular data of the proteins involved are manifold but t... Read more
Dominik Harant and Ingeborg Lang
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
Inconel 718 (IN718) is the most popular precipitation-strengthened nickel-based superalloy introduced by the Huntington Alloys Division of INCO in 1959 (Ref Read more
Oskar Dziuba, Grzegorz Cempura, Agnieszka Wusatowska-Sarnek & Adam Kruk
A solid oxide fuel cell (SOFC) is an electrochemical device that converts the chemical energy of hydrogen directly into electricity. A single cell usually has a form of a flat plate in which an impervious and dense ion-conducting electrolyte is sandwiched between two porous catalytic electrodes: an anode and a cathode. Fuel is fed to the anode side, and the air is supplied to the cathode. The gasses cannot mix to avoid unproductive combustion. Instead, gasses hit catalyst material, lose their... Read more
Grzegorz Brus, Hiroshi Iwai, Janusz S. Szmyd
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
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
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
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
Edwin Peng, Alexander Roth, Craig A. Zuhlke, Soodabeh Azadehranjbar, Dennis R. Alexander, George Gogos, Jeffrey E. Shield
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
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
Despite the importance of studying the instability of delithiated cathode materials, it remains difficult to underpin the degradation mechanism of lithium-rich cathode materials due to the complication of combined chemical and structural evolutions. Herein, we use state-of-the-art electron microscopy tools, in conjunction with synchrotron X-ray techniques and first-principle calculations to study a 4d-element-containing compound, Li2Ru0.5Mn0.5O3. We find surprisingly, after cycling, ruthenium... Read more
Lin, Ruoqian AU - Hu, Enyuan AU - Liu, Mingjie AU - Wang, Yi AU - Cheng, Hao AU - Wu, Jinpeng AU - Zheng, Jin-Cheng AU - Wu, Qin AU - Bak, Seongmin AU - Tong, Xiao AU - Zhang, Rui AU - Yang, Wanli AU - Persson, Kristin A. AU - Yu, Xiqian AU - Yang, Xiao-Qing AU - Xin, Huolin L. PY
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.Read more
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
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…Read more
Christian Boedeker, Margarete Schüler, Greta Reintjes, Olga Jeske, Muriel C. F. van Teeseling et al.