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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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
The microstructure morphologies have been characterized by high resolution laboratory X-ray computed tomography in Carbon Fiber Reinforced Carbon and Silicon Carbide (C/C-SiC) ceramic composites fabricated by Gaseous Silicon Infiltration (GSI) from C/C preforms of three different architectures: 3D stitched cloth fabric; 3D orthogonal woven fabric; and needled short-cut felt. Each composites’ microstructure was influenced by the structure of the C/C preform. By incorporating tomography with ... Read more
Fan Wan, Talha, J. Pirzada, Rongjun Liu, Yanfei Wang, Changrui Zhang, Thomas James Marrow
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.
Mitochondria undergo spontaneous transient elevations in matrix pH associated with drops in mitochondrial membrane potential. These mitopHlashes require a functional respiratory chain and the profusion protein optic atrophy 1, but their mechanistic basis is unclear. To gain insight on the origin of these dynamic events, we resolved the ultrastructure of flashing mitochondria by correlative light and electron microscopy. HeLa cells expressing the matrix-targeted pH probe mitoSypHer were screen... Read more
Manon Rosselin, Paula Nunes-Hasler, and Nicolas Demaurex
With the advent of neurogenetic methods, the neural basis of behavior is presently being analyzed in more and more detail. This is particularly true for visually driven behavior of Drosophila melanogaster where cell-specific driver lines exist that, depending on the combination with appropriate effector genes, allow for targeted recording, silencing and optogenetic stimulation of individual cell-types. Together with detailed connectomic data of large parts of the fly optic lobe, this has rece... Read more
Kevin M. Boergens , Christoph Kapfer, Moritz Helmstaedter, Winfried Denk, Alexander Borst
Analysis of neuronal arborization and connections is a powerful tool in fundamental and clinical neuroscience. Changes in neuronal morphology are central to brain development and plasticity and are associated with numerous diseases. Golgi staining is a classical technique based on a deposition of metal precipitate in a random set of neurons. Despite their versatility, Golgi methods have limitations that largely precluded their use in advanced microscopy. We combined Golgi staining with fluore... Read more
Katlijn Vints, Dorien Vandael, Pieter Baatsen, Benjamin Pavie, Frank Vernaillen, Nikky Corthout, Vasily Rybakin, Sebastian Munck & Natalia V. Gounko
We investigated the synaptic innervation of apical tufts of cortical pyramidal cells in a region between layers 1 and 2 using 3-D electron microscopy (3D-EM) applied to four cortical regions in mouse. Across all cortices, we found the relative inhibitory input at the apical dendrite’s main bifurcation to be more than 3-fold stronger for layer 2 pyramidal cells than for all other pyramidal cells. Towards the distal tuft dendrites in upper layer 1, however, the relative inhibitory input was a... Read more
Ali Karimi, Jan Odenthal, Florian Drawitsch, Kevin M. Boergens, Moritz Helmstaedter
The major mammalian bloodstream form of the African sleeping sickness parasite Trypanosoma bruceimultiplies rapidly, and it is important to understand how these cells divide. Organelle inheritance involves complex spatiotemporal re-arrangements to ensure correct distribution to daughter cells…Read more
Louise Hughes, Samantha Borrett, Katie Towers, Tobias Starborg, Sue Vaughan
Podocytes present a unique 3D architecture specialized for glomerular filtration. However, several 3D morphological aspects on podocyte development remain partially understood because they are difficult to reveal using conventional scanning electron microscopy (SEM). Here, we adopted serial block-face SEM imaging…Read more
Koichiro Ichimura, Soichiro Kakuta, Yuto Kawasaki, Takayuki Miyaki, Takahiro Nonami, Naoyuki Miyazaki, Tomoyo Nakao, Sakiko Enomoto, Shigeo Arai, Masato Koike, Kazuyoshi Murata, Tatsuo Sakai
Neurons project axons to local and distal sites and can display heterogeneous morphologies with limited physical dimensions that may influence the structure of large organelles such as mitochondria. Using cryo-electron tomography (cryo-ET), we characterized native environments within axons and presynaptic varicosities to examine whether spatial restrictions within these compartments influence the morphology of mitochondria. Segmented tomographic reconstructions revealed distinctive morphologi... Read more
Tara D. Fischer, Pramod K. Dash, Jun Liu, M. Neal Waxham
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
It is well known that the phonatory process changes during the life span. However, detailed investigations on potential factors concerned are rare. To deal with this issue, we performed extended biomechanical, macro anatomical, and histological analyses of the contributing laryngeal structures in ex vivo juvenile sheep models. Altogether twelve juvenile sheep larynges were analyzed within the phonatory experiments. Three different elongation levels and 16 different flow levels were applied to... Read more
Michael Döllinger, Olaf Wendler, Claus Gerstenberger, Tanja Grossmann, Marion Semmler, Hossein Sadeghi, and Markus Gugatschka
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.
Computer-aided visualization and analysis has revolutionized the study of fossils. Fossils can now be characterized in three dimensions and in unprecedented detail. The resulting digital reconstructions can be used in rigorous functional analyses. Hypotheses regarding the function of extinct organisms can therefore be tested.Read more
Trends in Ecology & Evolution
Under the armor: X-ray computed tomographic reconstruction of the internal skeleton of Coahomasuchus chathamensis (Archosauria: Aetosauria) from the Upper Triassic of North Carolina, USA, and a phylogenetic analysis of Aetosauria
Aetosauria is a clade of heavily armored, quadrupedal omnivorous to herbivorous archosaurs known from the Late Triassic across what was the supercontinent of Pangea. Their abundance in many deposits relative to the paucity of other Triassic herbivores indicates that they were key components of Late Triassic ecosystems. However, their evolutionary relationships remain contentious due, in large part, to their extensive dermal armor, which often obstructs observation of internal skeletal anatomy... Read more
Devin K. Hoffman, Andrew B. Heckert, Lindsay E. Zanno