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.

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.

High-resolution characterization of centriole distal appendage morphology and dynamics by correlative STORM and electron microscopy

High-resolution characterization of centriole distal appendage morphology and dynamics by correlative STORM and electron microscopy

Centrioles are vital cellular structures that form centrosomes and cilia. The formation and function of cilia depends on a set of centriole’s distal appendages. In this study, we use correlative super resolution and electron microscopy to precisely determine where distal appendage proteins localize in relation to the centriole microtubules and appendage electron densities. Here we characterize a novel distal appendage protein ANKRD26 and detail, in high resolution, the initial steps of dist... Read more

Mathew Bowler, Dong Kong, Shufeng Sun, Rashmi Nanjundappa, Lauren Evans, Veronica Farmer, Andrew Holland, Moe R. Mahjoub, Haixin Sui & Jadranka Loncarek

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Cardiogenic Airflow in the Lung Revealed Using Synchrotron-Based Dynamic Lung Imaging

Cardiogenic Airflow in the Lung Revealed Using Synchrotron-Based Dynamic Lung Imaging

The beating heart is known to produce pressure and airflow oscillations in the lungs of mammals. This phenomenon is often disregarded as detailed measurement of its effects in the lung have hitherto not been possible. Previous studies have attempted to measure the effect of these oscillations on gas mixing. However, the results have proven inconclusive, due to the lack of a direct measurement tool capable of flow measurement throughout the entire bronchial tree. Here we present the first deta... Read more

Stephen Dubsky, Jordan Thurgood, Andreas Fouras, Bruce R. Thompson & Gregory J. Sheard

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Multiscale Co‐reconstruction of Lung Architectures and Inhalable Materials Spatial Distribution

Multiscale Co‐reconstruction of Lung Architectures and Inhalable Materials Spatial Distribution

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

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Microstructure analysis and image-based modelling of face masks for COVID-19 virus protection

Microstructure analysis and image-based modelling of face masks for COVID-19 virus protection

Until March 2021, around 120 million coronavirus disease (COVID-19) infected cases and over 2.6 million deaths have been reported worldwide. […] Recent investigations have implied that face masks help to reduce the disease transmission and therefore slow down the growth of the epidemic curve. However, there are still ongoing debates on the efficacy of wearing masks […] since there is a general lack of information relating to the material structure of commonly used face masks.Read more

Wenjia Du, Francesco Iacoviello, Tacson Fernandez, Rui Loureiro, Daniel J. L. Brett & Paul R. Shearing

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The visible skeleton 2.0: phenotyping of cartilage and bone in fixed vertebrate embryos and foetuses based on X-ray microCT

The visible skeleton 2.0: phenotyping of cartilage and bone in fixed vertebrate embryos and foetuses based on X-ray microCT

For decades, clearing and staining with Alcian Blue and Alizarin Red has been the gold standard to image vertebrate skeletal development. Here, we present an alternate approach to visualise bone and cartilage based on X-ray microCT imaging, which allows the collection of genuine 3D data of the entire developing skeleton at micron resolution.

Our novel protocol is based on ethanol fixation and staining with Ruthenium Red, and efficiently contrasts cartilage matrix, as demonstrated in wh... Read more

Simone Gabner, Peter Böck, Dieter Fink, Martin Glösmann, Stephan Handschuh

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Growth and cellular patterning during fetal human inner ear development studied by a correlative imaging approach

Growth and cellular patterning during fetal human inner ear development studied by a correlative imaging approach

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

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3D analysis of enamel demineralisation in human dental caries using high-resolution, large field of view synchrotron X-ray micro-computed tomography

3D analysis of enamel demineralisation in human dental caries using high-resolution, large field of view synchrotron X-ray micro-computed tomography

 

Unprecedented combination of resolution, field of view and contrast for the analysis human enamel carious lesions was achieved. Synchrotron X-ray micro-computed tomography revealed sub-micron details of enamel rod and inter-rod regions inaccessible by laboratory tomography. Successful segmentation and labelling allowed the extraction of enamel etching patterns and statistics. Correlation was obtained between synchrotron X-ray micro-tomography and FIB-SEM cross-sec... Read more

Cyril Besnard, Robert A. Harper, Thomas E. J. Moxham, Jonathan D. James, Malte Storm, Enrico Salvati, Gabriel Landini, Richard M. Shelton, Alexander M.Korsunsky

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Scientists use Avizo to capture the complex dynamics of particle movement in granular materials

Scientists use Avizo to capture the complex dynamics of particle movement in granular materials

Scientists have for the first time captured the complex dynamics of particle movement in granular materials, helping to explain why mixed nuts often see the larger Brazil nuts gather at the top. This phenomenon, known as the ‘Brazil-nut effect’, has huge implications for industries where uneven mixing can critically degrade product quality. The findings could have vital impact on industries struggling with the phenomenon, such as pharmaceuticals and mining.

For th... Read more

Parmesh Gajjar, Chris G. Johnson, James Carr, Kevin Chrispeels, J. M. N. T. Gray & Philip J. Withers

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Mitochondria-rough-ER contacts in the liver regulate systemic lipid homeostasis

Mitochondria-rough-ER contacts in the liver regulate systemic lipid homeostasis

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

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Combined quantitative microscopy on the microstructure and phase evolution in Li Al Ti (PO4) ceramics

Combined quantitative microscopy on the microstructure and phase evolution in Li Al Ti (PO4) ceramics

Lithium aluminum titanium phosphate (LATP) is one of the materials under consideration as an electrolyte in future all-solid-state lithium-ion batteries. In ceramic processing, the presence of secondary phases and porosity play an important role. In a presence of more than one secondary phase and pores, image analysis must tackle the difficulties about distinguishing between these microstructural features. In this study, we study the phase evolution of LATP ceramics sintered at temperatures b... Read more

Deniz Cihan GUNDUZ, Roland SCHIERHOLZ, Shicheng YUa, Hermann TEMPEL, Hans KUNGL, Rüdiger-A. EICHEL

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An Anisotropic Microstructure Evolution in a Solid Oxide Fuel Cell Anode

An Anisotropic Microstructure Evolution in a Solid Oxide Fuel Cell Anode

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

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A Neutron Tomographic Analysis of Plated Silver Coins from Ancient Greece Official or Illegal?

A Neutron Tomographic Analysis of Plated Silver Coins from Ancient Greece Official or Illegal?

In the 6th century BC different techniques of coin manufacture were employed by mints in mainland Greece and in the Greek colonies in Southern Italy. In Greece these techniques were evidently derived from the Lydians and consisted in striking a piece of cast metal of predetermined weight (a ‘blank’ or flan) between two engraved dies made of hardened bronze. Colonies in Magna Graecia, however, uniquely developed another set of minting techniques to produce what today is called incuse coina... Read more

Scott Olsen, Filomena Silvemini, Ulf Garbe, Max Avdeev, Joel Davis, Vladimir Luzin, Ken Sheedy

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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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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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Experimental study on the cracking process of layered shale using X-ray microCT

Experimental study on the cracking process of layered shale using X-ray microCT

The cracking process in Longmaxi formation shale was experimentally studied during uniaxial compressive loading. Both the evolution of the three-dimensional fracture network and the micromechanics of failure in the layered shale were examined as a function of the inclination angle of the bedding plane. To visualize the cracking process, the test devices presented here used an industrial X-ray CT scanner that enabled scanning during the uniaxial compressive loading. Scanning electron microscop... Read more

Institue of Geomechanic, Chinese Academy of Geological Sciences, Laboratory of Shale Oil & Gas, Beijing, China

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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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High-Resolution 3D FIB-SEM Image Analysis and Validation of Numerical Simulations of Nanometre-Scale Porous Ceramic with Comparisons to Experimental Results

High-Resolution 3D FIB-SEM Image Analysis and Validation of Numerical Simulations of Nanometre-Scale Porous Ceramic with Comparisons to Experimental Results

The development of focused ion beam-scanning electron microscopy (FIB-SEM) techniques has allowed high-resolution 3D imaging of nanometre-scale porous materials. These systems are of important interest to the oil and gas sector, as well as for the safe long-term storage of carbon and nuclear waste. This work focuses on validating the accurate representation of sample pore space in FIB-SEM-reconstructed volumes and the predicted permeability of these systems from subsequent single-phase flow s... Read more

Department of Chemical Engineering, Qatar Carbonates and Carbon Storage Research Centre, Imperial College London | Department of Applied Mathematics and Theoretical Physics, Cambridge University

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Anomalous metal segregation in lithium-rich material provides design rules for stable cathode in lithium-ion battery

Anomalous metal segregation in lithium-rich material provides design rules for stable cathode in lithium-ion battery

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

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Spatially resolved ultrasound diagnostics of Li-ion battery electrodes

Spatially resolved ultrasound diagnostics of Li-ion battery electrodes

The importance of reliable battery diagnostic systems has grown substantially in recent years as a result of the use of high power Li-ion battery packs in an increasingly diverse range of applications. Here, spatially resolved ultrasound acoustic measurements are used to analyse the condition of Li-ion electrodes. Ultrasonic measurements are performed on a commercial mobile phone battery over the full operating voltage window with the lithiation and delithiation of electrodes o... Read more

James B. Robinson, Maximilian Maier , George Alster , Tomos Compton , Dan J. L. Brett and Paul R. Shearing

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Deep nuclear invaginations are linked to cytoskeletal filaments – integrated bioimaging of epithelial cells in 3D culture

Deep nuclear invaginations are linked to cytoskeletal filaments – integrated bioimaging of epithelial cells in 3D culture

The importance of context in regulation of gene expression is now an accepted principle; yet the mechanism by which the microenvironment communicates with the nucleus and chromatin in healthy tissues is poorly understood. A functional role for nuclear and cytoskeletal architecture is suggested by the phenotypic differences observed between epithelial and mesenchymal cells…

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Danielle M. Jorgens, Jamie L. Inman, Michal Wojcik, Claire Robertson, Hildur Palsdottir, Wen-Ting Tsai, Haina Huang, Alexandre Bruni-Cardoso, Claudia S. López, Mina J. Bissell, Ke Xu, Manfred Auer

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