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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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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Membrane architecture of pulmonary lamellar bodies revealed by post-correlation on-lamella cryo-CLEM

Membrane architecture of pulmonary lamellar bodies revealed by post-correlation on-lamella cryo-CLEM

Lamellar bodies (LBs) are surfactant rich organelles in alveolar type 2 cells. LBs disassemble into a lipid-protein network that reduces surface tension and facilitates gas exchange at the air-water interface in the alveolar cavity. Current knowledge of LB architecture is predominantly based on electron microscopy studies using disruptive sample preparation methods. We established a post-correlation on-lamella cryo-correlative light and electron microscopy approach for cryo-FIB milled lung ce... Read more

Steffen Klein, Benedikt H. Wimmer, Sophie L. Winter, Androniki Kolovou, Vibor Laketa, Petr Chlanda

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Influence of Isothermal Holding on the Microstructure and Mechanical Properties of Electron Beam Welded Dissimilar Inconel 718/ATI 718Plus® Joint

Influence of Isothermal Holding on the Microstructure and Mechanical Properties of Electron Beam Welded Dissimilar Inconel 718/ATI 718Plus® Joint

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

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Cryo-STEM mapping of solid–liquid interfaces and dendrites in lithium-metal batteries

Cryo-STEM mapping of solid–liquid interfaces and dendrites in lithium-metal batteries

Solid–liquid interfaces are important in a range of chemical, physical and biological processes but are often not fully understood owing to the lack of high-resolution characterization methods that are compatible with both solid and liquid components. For example, the related processes of dendritic deposition of lithium metal and the formation of solid–electrolyte interphase layers are known to be key determinants of battery safety and performance in high-energy-density lithium-metal bat... Read more

Michael J. Zachman, Zhengyuan Tu, Snehashis Choudhury, Lynden A. Archer & Lena F. Kourkoutis

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Porous Metal–Organic Frameworks for Enhanced Performance Silicon Anodes in Lithium-Ion Batteries

Porous Metal–Organic Frameworks for Enhanced Performance Silicon Anodes in Lithium-Ion Batteries

Maintaining the physical integrity of electrode microstructures in Li-ion batteries is critical to significantly extend their cycle life. This is especially important for high-capacity anode materials such as silicon, whose operational volume expansion exerts huge internal stress within the anode, resulting in electrode destruction and capacity fade. In this study, we demonstrate that by incorporating metal–organic frameworks (MOFs) with carboxylate organic linkers into Si-based anodes, a s... Read more

Romeo Malik, Melanie. J. Loveridge, Luke J. Williams, Qianye Huang, Geoff West, Paul R. Shearing, Rohit Bhagat, Richard I. Walton

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Nanoporous Aluminum by Galvanic Replacement: Dealloying and Inward-Growth Plating

Nanoporous Aluminum by Galvanic Replacement: Dealloying and Inward-Growth Plating

In aqueous solutions, electro/chemically deposited metals usually grow outward into electrolyte. Here we report that the reduced Al grows inward into the sample, surprisingly, while Mg (in pure Mg and Al2Mg3 alloy) is galvanically replaced with Al in an ionic liquid. The galvanic replacement reaction (GRR) of Al2Mg3 involves a dealloying process that generates a nanoporous Al skeleton, and simultaneously the inward-growth plating of Al that thicke... Read more

Wei Yang, Xian-Gui Zheng, Shao-Gang Wang, Hai-Jun Jin

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Microstructural evolution and deformation behavior of Al-Cu alloys: A Transmission X-ray Microscopy (TXM) and micropillar compression study

Microstructural evolution and deformation behavior of Al-Cu alloys: A Transmission X-ray Microscopy (TXM) and micropillar compression study

A unique approach to correlating an evolving 3D microstructure in an Al-Cu alloyand its micro-scale mechanical properties has been introduced. Using these nanoscale three-dimensional microstructures derived from Transmission X-rayMicroscopy (TXM), individual contributions from different strengthening mechanisms were quantified. The spatial distribution and morphology of the individual θ′ and θ phases were seen to play an important role in influencing dislocation storage. Uniaxi... Read more

C. Shashank Kaira, Christopher Kantzos, Jason J. Williams, Vincent De Andrade, Francesco De Carlo, Nikhilesh Chawlaa

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Aging of a Pt/Al2O3 exhaust gas catalyst monitored by quasi in situ X-ray micro computed tomography

Aging of a Pt/Al2O3 exhaust gas catalyst monitored by quasi in situ X-ray micro computed tomography

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

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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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Structure of the Ty3/Gypsy retrotransposon capsid and the evolution of retroviruses

Structure of the Ty3/Gypsy retrotransposon capsid and the evolution of retroviruses

Retroviruses evolved from long terminal repeat (LTR) retrotransposons by acquisition of envelope functions, and subsequently reinvaded host genomes. Together, endogenous retroviruses and LTR retrotransposons represent major components of animal, plant, and fungal genomes. Sequences from these elements have been exapted to perform essential host functions, including placental development, synaptic communication, and transcriptional regulation. They encode a Gag polypeptide, the capsid domains ... Read more

Svetlana O. Dodonova, Simone Prinz, Virginia Bilanchone, Suzanne Sandmeyer, and John A. G. Briggs

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Differentiation and Characterization of Excitatory and Inhibitory Synapses by Cryo-electron Tomography and Correlative Microscopy

Differentiation and Characterization of Excitatory and Inhibitory Synapses by Cryo-electron Tomography and Correlative Microscopy

As key functional units in neural circuits, different types of neuronal synapses play distinct roles in brain information processing, learning, and memory. Synaptic abnormalities are believed to underlie various neurological and psychiatric disorders. Here, by combining cryo-electron tomography and cryo-correlative light and electron microscopy, we distinguished intact excitatory and inhibitory synapses of cultured hippocampal neurons, and visualized the in situ 3D organization of ... Read more

Chang-Lu Tao, Yun-Tao Liu, Rong Sun, Bin Zhang, Lei Qi, Sakar Shivakoti, Chong-Li Tian, Peijun Zhang, Pak-Ming Lau, Z. Hong Zhou and Guo-Qiang Bi

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Cerebral Corpora amylacea are dense membranous labyrinths containing structurally preserved cell organelles

Cerebral Corpora amylacea are dense membranous labyrinths containing structurally preserved cell organelles

Corpora amylacea are cell-derived structures that appear physiologically in the aged human brain. While their histological identification is straightforward, their ultrastructural composition and microenvironment at the nanoscale have remained unclear so far, as has their relevance to aging and certain disease states that involve the sequestration of toxic cellular metabolites. Here, we apply correlative serial block-face scanning electron microscopy and transmission electron tomograp... Read more

Paula P. Navarro, Christel Genoud, Daniel Castaño-Díez, Alexandra Graff-Meyer, Amanda J. Lewis, Yvonne de Gier, Matthias E. Lauer, Markus Britschgi, Bernd Bohrmann, Stephan Frank, Jürgen Hench, Gabriel Schweighauser, Annemieke J. M. Rozemuller, Wilma D. J. van de Berg, Henning Stahlberg & Sarah H. Shahmoradian

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Three-dimensional imaging of the intracellular assembly of a functional viral RNA replicase complex

Three-dimensional imaging of the intracellular assembly of a functional viral RNA replicase complex

Positive-strand RNA viruses, which can be devastating pathogens in humans, animals and plants, replicate their genomes on intracellular membranes. Here, we describe the three-dimensional ultrastructural organization of a tombusvirus replicase in yeast, a valuable model for exploring virus–host interactions…

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Isabel Fernández de Castro, José J. Fernández, Daniel Barajas, Peter D. Nagy, Cristina Risco

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Fast and precise targeting of single tumor cells in vivo by multimodal correlative microscopy

Fast and precise targeting of single tumor cells in vivo by multimodal correlative microscopy

Intravital microscopy provides dynamic understanding of multiple cell biological processes, but its limited resolution has so far precluded structural analysis. Because it is difficult to capture rare and transient events, only a few attempts have been made to observe specific developmental and pathological processes in animal models using electron microscopy. The multimodal correlative approach that we propose here combines intravital microscopy, microscopic X-ray computed tomography and thr... Read more

Matthia A. Karreman, Luc Mercier, Nicole L. Schieber, Gergely Solecki, Guillaume Allio, Frank Winkler, Bernhard Ruthensteiner, Jacky G. Goetz, Yannick Schwab

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Chromosome segregation occurs by microtubule pushing in oocytes

Chromosome segregation occurs by microtubule pushing in oocytes

During cell division, spindle microtubules ensure an equal repartition of chromosomes between the two daughter cells. While the kinetochore-dependent mechanisms that drive mitotic chromosome segregation are well understood, in oocytes of most species atypical spindles assembled in absence of centrosomes entail poorly understood mechanisms of chromosome segregation. In particular, the structure(s) responsible for force generation during meiotic chromosome separation in oocytes is unclear. Usin... Read more

Kimberley Laband, Rémi Le Borgne, Frances Edwards, Marine Stefanutti, Julie C. Canman, Jean-Marc Verbavatz, Julien Dumont

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3D electron tomography of brain tissue unveils distinct Golgi structures that sequester cytoplasmic contents in neurons

3D electron tomography of brain tissue unveils distinct Golgi structures that sequester cytoplasmic contents in neurons

Macroautophagy is morphologically characterized by autophagosome formation. Autophagosomes are double-membraned vesicles that sequester cytoplasmic components for further degradation in the lysosome. Basal autophagy is paramount for intracellular quality control in post-mitotic cells but, surprisingly, the number of autophagosomes in post-mitotic neurons is very low, suggesting that alternative degradative structures could exist in neurons…

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Maria Rosario Fernandez-Fernandez, Desire Ruiz-Garcia, Eva Martin-Solana, Francisco Javier Chichon, Jose L. Carrascosa, Jose-Jesus Fernandez

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A correlative approach for combining microCT, light and transmission electron microscopy in a single 3D scenario

A correlative approach for combining microCT, light and transmission electron microscopy in a single 3D scenario

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 and Bernhard Ruthensteiner

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A global approach for quantitative super resolution and electron microscopy on cryo and epoxy sections using self-labeling protein tags

A global approach for quantitative super resolution and electron microscopy on cryo and epoxy sections using self-labeling protein tags

Correlative light and electron microscopy (CLEM) is a powerful approach to investigate the molecular ultrastructure of labeled cell compartments. However, quantitative CLEM studies are rare, mainly due to small sample sizes and the sensitivity of fluorescent proteins to strong fixatives and contrasting reagents for EM. Here, we show that fusion of…

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Andreas Müller, Martin Neukam, Anna Ivanova, Anke Sönmez, Carla Münster, Susanne Kretschmar, Yannis Kalaidzidis, Thomas Kurth, Jean-Marc Verbavatz & Michele Solimena

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Microtubule organization within mitotic spindles revealed by serial block face scanning electron microscopy and image analysis

Microtubule organization within mitotic spindles revealed by serial block face scanning electron microscopy and image analysis

Serial block face scanning electron microscopy (SBF-SEM) is a powerful method to analyze cells in 3D. Here, working at the resolution limit of the method, we describe a correlative light–SBF-SEM workflow to resolve microtubules of the mitotic spindle in human cells. We present four examples of uses for this workflow that are not practical by light microscopy and/or transmission electron microscopy. First, distinguishing closely associated microtubules within K-fibers; second, resolving brid... Read more

Faye M. Nixon, Thomas R. Honnor, Nicholas I. Clarke, Georgina P. Starling, Alison J. Beckett, Adam M. Johansen, Julia A. Brettschneider, Ian A. Prior, Stephen J. Royle

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Influenza A matrix protein M1 is sufficient to induce lipid membrane deformation

Influenza A matrix protein M1 is sufficient to induce lipid membrane deformation

The matrix protein M1 of the Influenza A virus is considered to mediate viral assembly and budding at the plasma membrane (PM) of infected cells. In order for a new viral particle to form, the PM lipid bilayer has to bend into a vesicle towards the extracellular side. Studies in cellular models have proposed that different viral proteins might be responsible for inducing membrane curvature in this context (including M1), but a clear consensus has not been reached. In this study, we use a comb... Read more

Ismail Dahmani, Kai Ludwig, Salvatore Chiantia

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Structural Evolution of Highly Active Multicomponent Catalysts for Selective Propylene Oxidation

Structural Evolution of Highly Active Multicomponent Catalysts for Selective Propylene Oxidation

Multicomponent Bi-Mo-Fe-Co oxide catalysts prepared via flame spray pyrolysis were tested for selective propylene oxidation, showing high conversion (>70%) and selectivity (>85%) for acrolein and acrylic acid at temperatures of 330 ◦C. During extended time-on-stream tests (5–7 days), the catalysts retained high activity while undergoing diverse structural changes. This was evident on: (a) the atomic scale, using powder X-ray diffraction, Raman spectroscopy, X-ray absorption spectros... Read more

Paul Sprenger, Thomas L Sheppard, Jussi-Petteri Suuronen, Abhijeet Gaur, Federico Benzi and Jan-Dierk Grunwaldt

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