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.
SiC-SiC ceramic matrix composites are candidate materials for fuel cladding in Generation IV nuclear fission reactors and as accident tolerant fuel clad in current generation plant.
Experimental methods are needed that can detect and quantify the development of mechanical damage, to support modelling and qualification tests for these critical components. In situ observations of damage development have been obtained of tensile and C-ring mechanical test specimens of a braided nuclear gr... Read more
L. Saucedo-Mora, T. Lowe, S. Zhao, P.D. Lee, P.M. Mummery, T.J. Marrow
TRISO particles, a composite nuclear fuel built up by ceramic and graphitic layers, have outstanding high temperature resistance. TRISO fuel is the key technology for High Temperature Reactors (HTRs) and the Generation IV Very High Temperature Reactor (VHTR) variant.
TRISO offers unparalleled containment of fission products and is extremely robust during accident conditions. An understanding of the thermal performance and mechanical properties of TRISO fuel requires a detailed knowledg... Read more
T. Lowe, R.S. Bradley, S. Yue, K. Barii, J. Gelb, N. Rohbeck, J. Turner, P.J. Withers
The appearance of wings in insects, early in their evolution , has been one of the more critical innovations contributing to their extraordinary diversity. Despite the conspicuousness and importance of wings, the origin of these structures has been difficult to resolve and represented one of the “abominable mysteries” in evolutionary biology . More than a century of debate has boiled the matter down to two competing alternatives—one of wings representing an extension of the thorac... Read more
Department of Zoology, Faculty of Science, Charles University, Praha, Czech Republic and al.
Evidence for macroscopic life in the Paleoproterozoic Era comes from 1.8 billion-year-old (Ga) compression fossils [Han TM, Runnegar B (1992) Science 257:232–235; Knoll et al. (2006) Philos Trans R Soc Lond B 361:1023–1038], Stirling biota [Bengtson S et al. (2007) Paleobiology 33:351–381], and large colonial organisms exhibiting signs of coordinated growth from the 2.1-Ga Francevillian series, Gabon. Here we report on pyritized string-shaped structures from... Read more
Abderrazak El Albani, M. Gabriela Mangano, Luis A. Buatois, Stefan Bengtson, Armelle Riboulleau, Andrey Bekker, Kurt Konhauser, Timothy Lyons, Claire Rollion-Bard, Olabode Bankole, Stellina Gwenaelle Lekele Baghekema, Alain Meunier, Alain Trentesaux, Arnaud Mazurier, Jeremie Aubineau, Claude Laforest, Claude Fontaine, Philippe Recourt, Ernest Chi Fru, Roberto Macchiarelli, Jean Yves Reynaud, François Gauthier-Lafaye, and Donald E. Canfield
We demonstrate feasibility of the workflow by combining in vivo 2-photon microscopy and focused ion beam scanning electron microscopy (FIB/SEM) to dissect the role of astrocytic coverage in the persistence of dendritic spines.
Emerging 3D correlative light and electron microscopy (CLEM) approaches enable studying neuronal structure-function relations at unprecedented depth and precision. However, established protocols for the correlation of light and electron micrographs rely ... Read more
Manja Luckner,Steffen Burgold, Severin Filser, Maximilian Scheungrab, Yilmaz Niyaz, Eric Hummel, Gerhard Wanner, Jochen Herms
Endosseous oral implant is applied for orthodontic anchorage in subjects with multiple tooth agenesis. Its effectiveness under orthodontic loading has been demonstrated clinically and experimentally. This study investigates the deformation and stress on the bone and implant for different bite forces by three-dimensional (3D) finite element (FE) methods. A numerical simulation of deformation and stress distributions around implants was used to estimate the survival life for implants. The model... Read more
Hsin-Chung Cheng, Boe-Yu Peng, May-Show Chen, Chiung-Fang Huang, Yi Lin, and Yung-Kang Shen
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
Masseter muscle function influences mandibular bone homeostasis. As previously reported, bone resorption markers increased in the mouse mandibular condyle two days after masseter paralysis induced with botulinum toxin type A (BoNTA), followed by local bone loss.
This study aimed to evaluate the bone quality of both the mandibular condyle and alveolar process in the mandible of adult mice during the early stage of a BoNTA‐induced masseter muscle atrophy, using a combined 3D histomorpho... Read more
Julián Balanta‐Melo, María Angélica Torres‐Quintana, Maximilian Bemmann, Carolina Vega, Constanza González, Kornelius Kupczik, Viviana Toro‐Ibacache, Sonja Buvinic
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
The clinical use of bioactive molecules in bone regeneration has been known to have side effects, which result from uncontrolled and supraphysiological doses.
In this study, we demonstrated the synergistic effect of two bioactive molecules, bone morphogenic protein-2 (BMP-2) and alendronate (ALN), by releasing them in a sequential manner. Collagen-hydroxyapatite composite scaffolds functionalized using BMP-2 are loaded with biodegradable microspheres where ALN is encapsulated.
Th... Read more
Dongtak Lee, Maierdanjiang Wufuer, Insu Kim, Tae Hyun Choi , Byung Jun Kim , Hyo Gi Jung, Byoungjun Jeon, Gyudo Lee, Ok Hee Jeon, Hak Chang & Dae Sung Yoon
Microscopic organisms that penetrate calcareous structures by actively dissolving the carbonate matrix, namely microendoliths, have an important influence on the breakdown of marine carbonates.
Microscopic organisms that penetrate calcareous structures by actively dissolving the carbonate matrix, namely microendoliths, have an important influence on the breakdown of marine carbonates. The study of these microorganisms and the bioerosion traces they produce is crucial for understanding ... Read more
Philipp-Konrad Schätzle, Max Wisshak, Andreas Bick, André Freiwald, Alexander Kieneke
The Braconidae are a megadiverse and ecologically highly important group of insects. The vast majority of braconid wasps are parasitoids of other insects, usually attacking the egg or larval stages of their hosts. The ovipositor plays a crucial role in the assessment of the potential host and precise egg laying. We used lightand electron-microscopic techniques to investigate all inherent cuticular elements of the ovipositor (the female 9th abdominal tergum, two pairs of valvifers, and three p... Read more
Michael Csader, Karin Mayer, Oliver Betz, Stefan Fischer, Benjamin Eggs
Micro-computed tomography (μCT) is a valuable imaging modality for longitudinal quantification of bone volumes to identify disease or treatment effects for a broad range of conditions that affect bone health. Complex structures, such as the hindpaw with up to 31 distinct bones in mice, have considerable analytic potential, but quantification is often limited to a single bone volume metric due to the intensive effort of manual segmentation. Herein, we introduce a high-throughput, user-friendl... Read more
H. Mark Kenney, Yue Peng, Kiana L.Chen, Raquel Ajalik, Lindsay Schnur, Ronald W.Wood, Edward M.Schwarz, Hani A. Awad
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.
Sarcomeres are force-generating and load-bearing devices of muscles. A precise molecular picture of how sarcomeres are built underpins understanding their role in health and disease. Here, we determine the molecular architecture of native vertebrate skeletal sarcomeres by electron cryo-tomography.
Our reconstruction reveals molecular details of the three-dimensional organization and interaction of actin and myosin in the A-band, I-band, and Z-disc and demonstrates that α-actinin cros... Read more
Zhexin Wang, Michael Grange, Thorsten Wagner, Ay Lin Kho, Mathias Gautel, Stefan Raunser
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
Malignant cells are surrounded by a complex and supportive tumor microenvironment that consists of immune cells, extracellular matrix, vasculature, and fibroblasts. Cancer-associated fibroblasts (CAF) are the major cell type in the reactive stroma and are known to promote tumorigenesis and metastasis. Fibroblast activation protein alpha (FAP) is a transmembrane serine protease expressed by CAFs in the microenvironment of epithelial tumors.
Meta-analysis of FAP expression and clinical ... Read more
Hallie M. Hintz, Joseph P. Gallant, Donald J. Vander Griend, Ilsa M. Coleman, Peter S. Nelson and Aaron M. LeBeau
Osteocytes are the most frequent bone cells connected with each other through cell processes within tiny tubular-shaped canaliculi. The so-called osteocyte lacunar-canalicular network (LCN) plays a crucial role in bone remodeling and mineral homeostasis. Given the critical nature of these functions, it is herein hypothesized that the LCN must be structurally “overengineered” to provide network resilience.
This hypothesis is tested by characterizing canalicular networks in human bon... Read more
Emely Bortel, Liam M Grover, Neil Eisenstein, Christian Seim, Heikki Suhonen, Alexandra Pacureanu, Peter Westenberger, Kay Raum, Max Langer, Francoise Peyrin, Owen Addison, Bernhard Hesse
Precise methods for quantifying drug accumulation in brain tissue are currently very limited, challenging the development of new therapeutics for brain disorders. Transcardial perfusion is instrumental for removing the intravascular fraction of an injected compound, thereby allowing for ex vivo assessment of extravasation into the brain. However, pathological remodeling of tissue microenvironment can affect the efficiency of transcardial perfusion, which has been largely overlooked.
We... Read more
Serhii Kostrikov, Kasper B. Johnsen, Thomas H. Braunstein, Johann M. Gudbergsson, Frederikke P. Fliedner, Elisabeth A. A. Obara, Petra Hamerlik, Anders E. Hansen, Andreas Kjaer, Casper Hempel & Thomas L. Andresen
Adipose models have been applied to mechanistic studies of metabolic diseases (such as diabetes) and the subsequent discovery of new therapeutics. However, typical models are either insufficiently complex (2D cell cultures) or expensive and labor intensive (mice/in vivo). To bridge the gap between these models and in order to better inform pre-clinical studies we have developed a drug-responsive 3D model of white adipose tissue (WAT).
Here, spheroids (680 ± 60 μm) comp... Read more
Alexander D Graham, Rajesh Pandey, Viktoriya S Tsancheva, Alessia Candeo, Stanley W Botchway, Alasdair J Allan, Lydia Teboul4, Kamel Madi, Tahkur S Babra, Louisa A K Zolkiewski, Xuan Xue, Liz Bentley, Joan Gannon, Sam N Olof and Roger D Cox
Ovarian cancer is the leading cause of death among gynecological cancers, but is poorly amenable to preoperative diagnosis. In this study, we investigate the feasibility of “optical biopsy,” using high-optical-resolution photoacoustic microscopy (OR-PAM) to quantify the microvasculature of ovarian and fallopian tube tissue. The technique is demonstrated using excised human ovary and fallopian tube specimens imaged immediately after surgery.
This report describes the first applicatio... Read more
Bin Rao, Xiandong Leng, Yifeng Zeng, Yixiao Lin, Ruimin Chen, Qifa Zhou, Andrea R. Hagemann, Lindsay M. Kuroki, Carolyn K. McCourt, David G. Mutch, Matthew A. Powell, Ian S. Hagemann & Quing Zhu