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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Progressive transformation of the otic placode into the functional inner ear during gestational development in humans leads to the acquisition of hearing perception via the cochlea and balance and spatial orientation via the vestibular organ.
Using a correlative approach involving micro-computerized tomography (micro-CT), transmission electron microscopy and histological techniques we were able to examine both the morphological and cellular changes associated with human inner ear devel... Read more
Lejo Johnson Chacko, David Wertjanz, Consolato Sergi, Jozsef Dudas, Natalie Fischer, Theresa Eberharter, Romed Hoermann, Rudolf Glueckert, Helga Fritsch, Helge Rask-Andersen, Anneliese Schrott-Fischer & Stephan Handschuh
In biomedical research, a huge variety of different techniques is currently available for the structural examination of small specimens, including conventional light microscopy (LM), transmission electron microscopy (TEM), confocal laser scanning microscopy (CLSM), microscopic X-ray computed tomography (microCT), and many others. Since every imaging method is physically limited by certain parameters, a correlative use of complementary methods often yields a significant broader range of inform... Read more
Stephan Handschuh, Natalie Baeumler, Thomas Schwaha & Bernhard Ruthensteiner
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
Shelled pteropods are widely regarded as bioindicators for ocean acidification, because their fragile aragonite shells are susceptible to increasing ocean acidity. While short-term incubations have demonstrated that pteropod calcification is negatively impacted by ocean acidification, we know little about net calcification in response to varying ocean conditions in natural populations. Here, we examine in situ calcification of Limacina helicina pteropods collected from the California... Read more
Lisette Mekkes, Willem Renema, Nina Bednaršek, Simone R. Alin, Richard A. Feely, Jef Huisman, Peter Roessingh & Katja T. C. A. Peijnenburg
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
Rapid implementation of global scale carbon capture and storage is required to limit temperature rises to 1.5 °C this century. Depleted oilfields provide an immediate option for storage, since injection infrastructure is in place and there is an economic benefit from enhanced oil recovery. To design secure storage, we need to understand how the fluids are configured in the microscopic pore spaces of the reservoir rock. We use high-resolution X-ray imaging to study the flow of oil, water and ... Read more
Abdulla Alhosani, Alessio Scanziani, Qingyang Lin, Ali Q. Raeini, Branko Bijeljic & Martin J. Blunt
The cleanliness of liquid steel is defined by the amounts of dissolved unwanted impurities and precipitated unwanted non-metallic phases.[…] Improving the cleanliness of the steel would mean a lower fraction of impurities in the final product. […] A novel approach, utilizing controlled synthetic inclusion/metal samples, has been developed to study the reactions between free inclusion-slag droplets and steel. The technique combines High-Temperature Confocal Scanning Laser Microscop... Read more
Akalya Raviraj, Nadia Kourra, Mark A. Williams, Gert Abbel, Claire Davis, Wouter Tiekink, Seetharaman Sridhar & Stephen Spooner
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
Wire arc additive manufacturing (WAAM) technology has attracted considerable interest in large-scale metallic components, but porosity and low deposition rate are the two dominating technical challenges in WAAM of aluminum alloy. In order to effectively solve these problems, a novel method of hot-wire arc additive manufacturing is used to fabricate aluminum alloy. Systematic studies are carried out to investigate the formation mechanism of the pores, the macro/microstructures, as well as the ... Read more
Rui Fu, Shuiyuan Tang, Jiping Lu, Yinan Cui, Zixiang Li, Haoru Zhang, Tianqiu Xu, Zhuo Chen, Changmeng Liu
Carbon dioxide emissions must be reduced significantly to limit the negative consequences of climate change. For this reason, fossil fuels must be replaced by renewable energy sources. However, wind and solar energy, for example, are sporadic sources and, thus, not inevitably available when needed. This results in periods of energy surplus and shortage, which are not necessarily predictable. Hence, energy storage concepts are required to compensate for these fluctuations, thereby retaining en... Read more
Sebastian Weber, Ken L. Abel, Ronny T. Zimmermann, Xiaohui Huang, Jens Bremer, Liisa K. Rihko-Struckmann, Darren Batey, Silvia Cipiccia, Juliane Titus, David Poppitz, Christian Kübel, Kai Sundmacher, Roger Gläser, Thomas L. Sheppard
Decommissioning of the damaged Chernobyl nuclear reactor Unit 4 is a top priority for the global community. Before such operations begin, it is crucial to understand the behaviour of the hazardous materials formed during the accident. Since those materials formed under extreme and mostly unquantified conditions, modelling alone is insufficient to accurately predict their physical, chemical and, predominantly, mechanical behaviour. Meanwhile, knowledge of the mechanical characteristics of thos... Read more
C.Paraskevoulakos, J.P.Forna-Kreutzer, K.R.Hallam, C.P.Jones, T.B.Scott, C.Gausse, D.J.Bailey, C.A.Simpson, D.Liu, C.Reinhard, C.L.Corkhill, M.Mostafavi
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
Since its invention and commercialization in the 1950s, ultra-high molecular weight polyethylene (UHMWPE) has been known as a high-performance polymer successfully applied in diverse engineering systems ranging from strong ropes for naval demands and wear-resistant liners in bearings, transportation belts and heavy trucks in mines and quarries, through the lining of chemical vessels and disposable bags in bioreactors, to sophisticated products such as orthopaedic implants and replacements of ... Read more
Eugene S. Statnik, Codrutza Dragu, Cyril Besnard, Alexander J.G. Lunt, Alexey I. Salimon, Aleksey Maksimkin and Alexander M. Korsunsky
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
Many of the grand challenges in volcanic and magmatic research are focused on understanding the dynamics of highly heterogeneous systems and the critical conditions that enable magmas to move or eruptions to initiate. However, we are usually unable to observe the processes directly. Here we give a short synopsis of the new capabilities and highlight the potential insights that in situ observation can provide. We present the first 3D data showing the evolving textural heterogeneity within a sh... Read more
Katherine J. Dobson1, Anja Allabar, Eloise Bretagne, Jason Coumans, Mike Cassidy, Corrado Cimarelli, Rebecca Coats, Thomas Connolley, Loic Courtois, Donald B. Dingwell, Danilo Di Genova, Benjamin Fernando, Julie L. Fife, Frey Fyfe, Stephan Gehne, Thomas Jones, Jackie E. Kendrick, Helen Kinvig, Stephan Kolzenburg, Yan Lavallée, Emma Liu, Edward W. Llewellin, Amber Madden-Nadeau, Kamel Madi, Federica Marone, Cerith Morgan, Julie Oppenheimer, Anna Ploszajski, Gavin Reid, Jenny Schauroth, Christian M. Schlepütz, Catriona Sellick, Jérémie Vasseur, Felix W. von Aulock, Fabian B. Wadsworth, Sebastian Wiesmaier and Kaz Wanelik
Amira capacities for membranes and filaments segmentation in cryo-TEM images are featured on the front cover of Biochemical Journal, July 2020.
Budding yeast septins are essential for cell division and polarity. (…) [The authors] have dissected, here, for the first time, the behavior of the Shs1 protomer bound to membranes at nanometer resolution, in complex with the other septins. Using electron microscopy, [the authors] have shown that on membranes, Shs1 protomers self-assembl... Read more
Cyntia Taveneau, Rémi Blanc, Gerard Pehau-Arnaudet, Aurélie Cicco, Aurélie Bertin
Through collaboration, the KAUST Visualization Core Lab (KVL) team augments the efforts and domain expertise of KAUST researchers by providing complimentary technical knowledge with exploratory visualization and analytic tools.
KVL’s multi-year collaboration with KAUST Distinguished Professor P. Magistretti and research scientist C. Calì’s KAUST-EPFL Alliance for Integrative Modelling of Brain Energy Metabolism project—itself a collaboration with the Swiss Blue Br... Read more
By the KAUST Visualization Core Lab team and Caitlin Clark
A key technique for controlling solidification microstructures is magneto-hydrodynamics (MHD), resulting from imposing a magnetic field to solidifying metals and alloys. Applications range from bulk stirring to flow control and turbulence damping via the induced Lorentz force. Over the past two decades the Lorentz force caused by the interaction of thermoelectric currents and a magnetic field, a MHD phenomenon known as Thermoelectric Magnetohydrodynamics (TEMHD), was also shown to drive inter... Read more
B. Cai, A. Kao, E. Boller, O.V. Magdysyuk, R.C. Atwood, N.T. Vo, K. Pericleous, P.D. Lee
In recent years, due to the rapid development of industrial lightweight technology, composite materials based on fiber reinforced plastics (FRP) have been widely used in the industry. However, the environmental impact of the FRPs is higher each year. To overcome this impact, co-injection molding could be one of the good solutions. But how to make the suitable control on the skin/core ratio and how to manage the glass fiber orientation features are still significant challenges. In this study, ... Read more
Chao-Tsai Huang, Xuan-Wei Chen, Wei-Wen Fu