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.
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The endoplasmic reticulum (ER) extends throughout a cell and plays a critical role in maintaining cellular homeostasis.
Changes in ER shape could provide a clue to explore the mechanisms that underlie the fate determination of neurons after
axon injury because the ER drastically changes its morphology under neuronal stress to maintain cellular homeostasis and
recover from damage. Because of their tiny structures and richness in the soma, the detailed morphology of the ER and... Read more
Mahmoud Elgendy,Hiromi Tamada, Takaya Taira, Yuma Iio, Akinobu Kawamura, Ayusa Kunogi, Yuka Mizutani, Hiroshi Kiyama
This study provides a comprehensive review of tortuosity and its impact on the transport properties of porous media. It discusses the classical theories and equations related to tortuosity for flow, conduction, and diffusion. The study also highlights the evolution of these theories and their connection to methodologies such as tomography and 3D image analysis. In order to clarify the topic, a new classification scheme and nomenclature for different types of tortuosity are proposed. The study... Read more
Holzer, L. *1, Marmet, P. 1, Fingerle, M. 2, Wiegmann, A. 2, Neumann, M. 3, Schmidt, V. 3
Three-Dimensional Architecture of Glomerular Endothelial Cells Revealed by FIB-SEM Tomography
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
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
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
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
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
Growing popularity and rapid development of Solid Oxide Fuel Cells (SOFCs) stem for their potential to become a gamechanger in the field of clean power generation technologies.
In this paper, a transient microstructure-oriented numerical simulation of a planar Direct Internal Reforming Solid Oxide Fuel Cell (DIR-SOFC) is delivered. The performance criteria in a direct steam reforming for a fuel starvation scenario are analyzed in order to optimize the underlying process. The proposed t... Read more
Maciej Chalusiak, Michal Wrobel, Marcin Mozdzierz, Katarzyna Berent, Janusz S. Szmyd, Shinji Kimijima, Grzegorz Brus
Mesoscale characterization of local property distributions in heterogeneous electrodes
The performance of electrochemical devices depends on the three-dimensional (3D) distributions of microstructural features in their electrodes. Several mature methods exist to characterize 3D microstructures over the microscale (tens of microns), which are useful in understanding homogeneous electrodes. However, methods that capture mesoscale (hundreds of microns) volumes at appropriate resolution (tens of nm) are lacking, though they are needed to understand more common, less ideal electrode... Read more
Tim Hsu, William K. Epting, Rubayyat Mahbub, Noel T. Nuhfer, Sudip Bhattachary, Yinkai Lei, Herbert M. Miller, Paul R. Ohodnicki, Kirk R. Gerdes, Harry W. Abernathy, Gregory A. Hackett, Anthony D. Rollett, Marc De Graef, Shawn Litster, Paul A. Salvador
Alternative battery technologies are required to meet growing energy demands and address the limitations of present technologies. As such, it is necessary to look beyond lithium-ion batteries. Zinc batteries enable high power density while being sourced from ubiquitous and cost-effective materials. This paper presents, for the first time known to the authors, multi-length scale tomography studies of failure mechanisms in zinc batteries with and without commercial microporous separators. In bo... Read more
Vladimir Yufit, Farid Tariq David S. Eastwood Moshiel Biton Billy Wu Peter D. Lee Nigel P. Brandon
A fully integrated, three-dimensional fluorescence to electron microscopy correlative workflow
While fluorescence microscopy provides tools for highly specific labeling and sensitive detection, its resolution limit and lack of general contrast has hindered studies of cellular structure and protein localization. Recent advances in correlative light and electron microscopy (CLEM), including the fully integrated CLEM workflow instrument, the Thermo Scientific CorrSight with MAPS, have allowed for a more reliable, reproducible, and quicker approach to correlate three-dimensional time-lapse... Read more
Claudia S. Lopez, Cedric Bouchet-Marquis, Christopher P. Arthur, Jessica L. Riesterer, Gregor Heiss, Guillaume Thibault, Lee Pullan, Sunjong Kwon, Joe W. Gray
Protocols for Generating Surfaces and Measuring 3D Organelle Morphology Using Amira
High-resolution 3D images of organelles are of paramount importance in cellular biology. Although light microscopy and transmission electron microscopy (TEM) have provided the standard for imaging cellular structures, they cannot provide 3D images.
However, recent technological advances such as serial block-face scanning electron microscopy (SBF-SEM) and focused ion beam scanning electron microscopy (FIB-SEM) provide the tools to create 3D images for the ultrastructural analysis of org... Read more
Edgar Garza-Lopez, Zer Vue, Prasanna Katti, Kit Neikirk, Michelle Biete, Jacob Lam, Heather K. Beasley, Andrea G. Marshall, Taylor A. Rodman, Trace A. Christensen, Jeffrey L. Salisbury, Larry Vang, Margaret Mungai, Salma Ash Shareef, Sandra A. Murray, Jianqiang Shao, Jennifer Streeter, Brian Glancy, Renata O. Pereira1, E. Dale Abel, and Antentor Hinton, Jr.
Automatic whole cell organelle segmentation in volumetric electron microscopy
Cells contain hundreds of different organelle and macromolecular assemblies intricately organized relative to each other to meet any cellular demands. Obtaining a complete understanding of their organization is challenging and requires nanometer-level, three-dimensional reconstruction of whole cells. Even then, the immense size of datasets and large number of structures to be characterized requires generalizable, automatic methods.
To meet this challenge, we developed an analy... Read more
Larissa Heinrich, Davis Bennett, David Ackerman, Woohyun Park, John Bogovic, View ORCID ProfileNils Eckstein, Alyson Petruncio, Jody Clements, C. Shan Xu, Jan Funke, Wyatt Korff, Harald F. Hess, Jennifer Lippincott-Schwartz, Stephan Saalfeld, Aubrey V. Weigel, COSEM Project Team
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies
Cortese et al. use integrative imaging techniques to generate a publicly available repository of morphological alterations induced by SARS-CoV-2 in lung cells. Accumulation of ER-derived double-membrane vesicles, the viral replication organelle, occurs concomitantly with cytoskeleton remodeling and Golgi fragmentation. Pharmacological alteration of cytoskeleton dynamics restricts viral replication and spread.
Pathogenesis induced by SARS-CoV-2 is thought to result from both an inflamma... Read more
Mirko Cortese, Ji-Young Lee, Berati Cerikan, ..., Laurent Chatel-Chaix, Yannick Schwab, Ralf Bartenschlager
Asymmetric Centriole Numbers at Spindle Poles Cause Chromosome Missegregation in Cancer
Chromosomal instability is a hallmark of cancer and correlates with the presence of extra centrosomes, which originate from centriole overduplication.
Overduplicated centrioles lead to the formation of centriole rosettes, which mature into supernumerary centrosomes in the subsequent cell cycle. While extra centrosomes promote chromosome missegregation by clustering into pseudo-bipolar spindles, the contribution of centriole rosettes to chromosome missegregation is unknown. We us... Read more
Marco R.Cosenza, Anna Cazzola, Annik Rossberg, Nicole L. Schieber, Gleb Konotop, Elena Bausch, Alla Slynko, Tim Holland-Letz, Marc S.Raab, Taronish Dubash, Hanno Glimm, Sven Poppelreuther, Christel Herold-Mende, Yannick Schwab, Alwin Krämer
Enamel caries is a highly prevalent worldwide disease that involves the demineralisation of the outer tooth structure. In this study, we report the analysis of artificially demineralised human enamel sections (‘slices’) etched using lactic acid (2% v/v) in comparison with healthy enamel using correlative techniques of optical and electron microscopy, as well as scanning diffraction. Demineralisation of the enamel was characterised at the micron to sub-micron scale. The structure of the he... 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
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
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
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
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