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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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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The Architecture of Traveling Actin Waves Revealed by Cryo-Electron Tomography

The Architecture of Traveling Actin Waves Revealed by Cryo-Electron Tomography

Actin waves are dynamic supramolecular structures involved in cell migration, cytokinesis, adhesion, and neurogenesis. Although wave-like propagation of actin networks is a widespread phenomenon, the actin architecture underlying wave propagation remained unknown. In situ cryo-electron tomography of Dictyostelium cells unveils the wave architecture and provides evidence for wave progression by de novo actin nucleation. Subtomogram averaging reveals the structu... Read more

Marion Jasnin, Florian Beck, Mary Ecke, Yoshiyuki Fukuda, Antonio Martinez-Sanchez, Wolfgang Baumeister, Günther Gerisch

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Influence of Copper Addition in AlSi7MgCu Alloy on Microstructure Development and Tensile Strength Improvement

Influence of Copper Addition in AlSi7MgCu Alloy on Microstructure Development and Tensile Strength Improvement

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

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Three-dimensional and microstructural fingerprinting of gold nanoparticles at fluid-mineral interfaces

Three-dimensional and microstructural fingerprinting of gold nanoparticles at fluid-mineral interfaces

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

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SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography

SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID19 pandemic, is a highly pathogenic β-coronavirus. As other coronaviruses, SARS-CoV-2 is enveloped, replicates in the cytoplasm and assembles at intracellular membranes. Here, we structurally characterize the viral replication compartment and report critical insights into the budding mechanism of the virus, and the structure of extracellular virions close to their native state by in situ cryo-electr... Read more

Steffen Klein, Mirko Cortese, Sophie L. Winter, Moritz Wachsmuth-Melm, Christopher J. Neufeldt, Berati Cerikan, Megan L. Stanifer, Steeve Boulant, Ralf Bartenschlager, Petr Chlanda

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3D Dissection of Structural Membrane-Wall Contacts in Filamentous Moss Protonemata

3D Dissection of Structural Membrane-Wall Contacts in Filamentous Moss Protonemata

Cell-to-cell contact is essential for communication and development of multicellular organisms. A prerequisite is the passage through membranes. That way, molecular exchange and information flow is regulated via hormones, membrane proteins and pores.
In plants, the rigid cell walls prevent large membrane contact areas between protoplasts. Only plasmodesmata, minute channels between adjacent cells, form direct connections. Often, molecular data of the proteins involved are manifold but t... Read more

Dominik Harant and Ingeborg Lang

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Multi-Scale Digital Image Correlation Analysis of In Situ Deformation of Open-Cell Porous Ultra-High Molecular Weight Polyethylene Foam

Multi-Scale Digital Image Correlation Analysis of In Situ Deformation of Open-Cell Porous Ultra-High Molecular Weight Polyethylene Foam

Since its invention and commercialization in the 1950s, ultra-high molecular weight polyethylene (UHMWPE) has been known as a high-performance polymer successfully applied in diverse engineering systems ranging from strong ropes for naval demands and wear-resistant liners in bearings, transportation belts and heavy trucks in mines and quarries, through the lining of chemical vessels and disposable bags in bioreactors, to sophisticated products such as orthopaedic implants and replacements of ... Read more

Eugene S. Statnik, Codrutza Dragu, Cyril Besnard, Alexander J.G. Lunt, Alexey I. Salimon, Aleksey Maksimkin and Alexander M. Korsunsky

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Quantifying Microstructural Evolution in Moving Magma

Quantifying Microstructural Evolution in Moving Magma

Many of the grand challenges in volcanic and magmatic research are focused on understanding the dynamics of highly heterogeneous systems and the critical conditions that enable magmas to move or eruptions to initiate. However, we are usually unable to observe the processes directly. Here we give a short synopsis of the new capabilities and highlight the potential insights that in situ observation can provide. We present the first 3D data showing the evolving textural heterogeneity within a sh... Read more

Katherine J. Dobson1, Anja Allabar, Eloise Bretagne, Jason Coumans, Mike Cassidy, Corrado Cimarelli, Rebecca Coats, Thomas Connolley, Loic Courtois, Donald B. Dingwell, Danilo Di Genova, Benjamin Fernando, Julie L. Fife, Frey Fyfe, Stephan Gehne, Thomas Jones, Jackie E. Kendrick, Helen Kinvig, Stephan Kolzenburg, Yan Lavallée, Emma Liu, Edward W. Llewellin, Amber Madden-Nadeau, Kamel Madi, Federica Marone, Cerith Morgan, Julie Oppenheimer, Anna Ploszajski, Gavin Reid, Jenny Schauroth, Christian M. Schlepütz, Catriona Sellick, Jérémie Vasseur, Felix W. von Aulock, Fabian B. Wadsworth, Sebastian Wiesmaier and Kaz Wanelik

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Synergistic role of nucleotides and lipids for the self-assembly of Shs1 septin oligomers

Synergistic role of nucleotides and lipids for the self-assembly of Shs1 septin oligomers

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

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High resolution X-ray computed tomography: A versatile non-destructive tool to characterize CFRP-based aircraft composite elements

High resolution X-ray computed tomography: A versatile non-destructive tool to characterize CFRP-based aircraft composite elements

The aim of the current study is to propose a versatile, non-destructive inspection strategy to evaluate the structure of two different aircraft carbon fibre reinforced polymer (CFRP) -based composite configurations, which are widely used for structural elements, respectively layered composite and sandwich structure. X-ray computed tomography (CT) has been used as a flexible method for assessment of porosity levels in CFRP components in both types of configuration, permitting to investigate th... Read more

Elena Dilonardo, Michele Nacucchi, Fabio De Pascalis, Mauro Zarrelli, Cinzia Giannini

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Revealing the mechanisms by which magneto-hydrodynamics disrupts solidification microstructures

Revealing the mechanisms by which magneto-hydrodynamics disrupts solidification microstructures

A key technique for controlling solidification microstructures is magneto-hydrodynamics (MHD), resulting from imposing a magnetic field to solidifying metals and alloys. Applications range from bulk stirring to flow control and turbulence damping via the induced Lorentz force. Over the past two decades the Lorentz force caused by the interaction of thermoelectric currents and a magnetic field, a MHD phenomenon known as Thermoelectric Magnetohydrodynamics (TEMHD), was also shown to drive inter... Read more

B. Cai, A. Kao, E. Boller, O.V. Magdysyuk, R.C. Atwood, N.T. Vo, K. Pericleous, P.D. Lee

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3D characterisation of dry powder inhaler formulations

3D characterisation of dry powder inhaler formulations

Carrier-based dry powder inhaler (DPI) formulations need to be accurately characterised for their particle size distributions, surface roughnesses, fines contents and flow properties. Understanding the micro-structure of the powder formulation is crucial, yet current characterisation methods give incomplete information. Commonly used techniques like laser diffraction (LD) and optical microscopy (OM) are limited due to the assumption of sphericity and can give variable results depending on par... Read more

P. Gajjar, I.D. Styliari, T.T.H. Nguyen, J. Carr, X. Chen, J.A. Elliott, R.B. Hammond, T.L. Burnett, K. Roberts, P.J. Withers, D.Murnane

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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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X-ray Micro-Computed Tomography of Polymer Electrolyte Fuel Cells: What is the Representative Elementary Area?

X-ray Micro-Computed Tomography of Polymer Electrolyte Fuel Cells: What is the Representative Elementary Area?

With the growing use of X-ray computed tomography (X-ray CT) datasets for modelling of transport properties, comes the need to define the representative elementary volume (REV) if considering three dimensions or the representative elementary area (REA) if considering two dimensions. The resolution used for imaging must be suited to the features of interest in the sample and the region-of-interest must be sufficiently large to capture key information. Polymer electrolyte fuel cells have a hier... Read more

Jennifer Hack et al 2020 J. Electrochem.

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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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Masseter muscle atrophy impairs bone quality of the mandibular condyle but not the alveolar process early after induction

Masseter muscle atrophy impairs bone quality of the mandibular condyle but not the alveolar process early after induction

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

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Micropore evolution in additively manufactured aluminum alloys under heat treatment and inter-layer rolling

Micropore evolution in additively manufactured aluminum alloys under heat treatment and inter-layer rolling

Additive manufacturing (AM) of aluminum alloy components has drawn broad attention from industrial customers in recent years. With the advantages of low cost and high deposition rate, wire + arc additive manufacturing (WAAM) has been recognized as a promising AM technology in producing large-scale aluminum alloy structural parts. However, the adverse effect of internal defects on mechanical properties has limited the application of WAAM aluminum alloys. Micropores, as one of the most harmfu... Read more

Jianglong Gu, Shouliang Yang, Minjie Gao, Jing Bai, Yuchun Zhai, Jialuo Ding

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Morphological evolution and internal strain mapping of pomelo peel using X-ray computed tomography and digital volume correlation

Morphological evolution and internal strain mapping of pomelo peel using X-ray computed tomography and digital volume correlation

Among natural cellular materials, pomelo peels, having a foam-like hierarchical microstructure, represent an ideal model for developing materials with high energy absorption efficiency. In this work, by combining X-ray tomographic imaging technique and digital volume correlation (DVC), in-situ stepwise uniaxial compression tests were performed to quantify the internal morphological evolution and kinematic responses of pomelo peel samples during compression.

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B.Wang, B.Pan, G.Lubineau

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