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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Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies

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

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Exploring confocal laser scanning microscopy (CLSM) and fluorescence staining as a tool for imaging and quantifying traces of marine microbioerosion and their trace-making microendoliths

Exploring confocal laser scanning microscopy (CLSM) and fluorescence staining as a tool for imaging and quantifying traces of marine microbioerosion and their trace-making microendoliths

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

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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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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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Multiple membrane extrusion sites drive megakaryocyte migration into bone marrow blood vessels

Multiple membrane extrusion sites drive megakaryocyte migration into bone marrow blood vessels

Platelets, cells central to hemostasis and thrombosis, are formed from parent cell megakaryocytes. Although the process is highly efficient in vivo, our ability to generate them in vitro is still remarkably inefficient. We proposed that greater understanding of the process in vivo is needed and used an imaging approach, intravital correlative light electron microscopy, to visualize platelet generation in bone marrow in the living mouse. In contrast to current understanding, we found that most... Read more

Edward Brown, Leo M Carlin, Claus Nerlov, Cristina Lo Celso, Alastair W Poole

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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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High-resolution characterization of centriole distal appendage morphology and dynamics by correlative STORM and electron microscopy

High-resolution characterization of centriole distal appendage morphology and dynamics by correlative STORM and electron microscopy

Centrioles are vital cellular structures that form centrosomes and cilia. The formation and function of cilia depends on a set of centriole’s distal appendages. In this study, we use correlative super resolution and electron microscopy to precisely determine where distal appendage proteins localize in relation to the centriole microtubules and appendage electron densities. Here we characterize a novel distal appendage protein ANKRD26 and detail, in high resolution, the initial steps of dist... Read more

Mathew Bowler, Dong Kong, Shufeng Sun, Rashmi Nanjundappa, Lauren Evans, Veronica Farmer, Andrew Holland, Moe R. Mahjoub, Haixin Sui & Jadranka Loncarek

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Soluble tubulin is locally enriched at mitotic centrosomes in C. elegans

Soluble tubulin is locally enriched at mitotic centrosomes in C. elegans

During mitosis, the centrosome expands its capacity to nucleate microtubules. Understanding the mechanisms of centrosomal microtubule nucleation is, however, constrained by a lack of knowledge of the amount of soluble and polymer tubulin at mitotic centrosomes. Here we combined light microscopy and serial-section electron tomography to measure the amount of dimer and polymer at mitotic centrosomes in early C. elegans embryos. We show that a C. elegans one-cell stage centrosome at metaphase co... Read more

Johannes Baumgart, Marcel Kirchner, Stefanie Redemann, Jeffrey Woodruff, Jean-Marc Verbavatz, Frank Julicher, Anthony Hyman, Thomas Mueller-Reichert, Jan Brugues

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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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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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Growth and cellular patterning during fetal human inner ear development studied by a correlative imaging approach

Growth and cellular patterning during fetal human inner ear development studied by a correlative imaging approach

Progressive transformation of the otic placode into the functional inner ear during gestational development in humans leads to the acquisition of hearing perception via the cochlea and balance and spatial orientation via the vestibular organ.

Using a correlative approach involving micro-computerized tomography (micro-CT), transmission electron microscopy and histological techniques we were able to examine both the morphological and cellular changes associated with human inner ear devel... Read more

Lejo Johnson Chacko, David Wertjanz, Consolato Sergi, Jozsef Dudas, Natalie Fischer, Theresa Eberharter, Romed Hoermann, Rudolf Glueckert, Helga Fritsch, Helge Rask-Andersen, Anneliese Schrott-Fischer & Stephan Handschuh

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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 & Bernhard Ruthensteiner

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Analysis of in vitro demineralised human enamel using multi-scale correlative optical and scanning electron microscopy, and high-resolution synchrotron wide-angle X-ray scattering

Analysis of in vitro demineralised human enamel using multi-scale correlative optical and scanning electron microscopy, and high-resolution synchrotron wide-angle X-ray scattering

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

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3D analysis of enamel demineralisation in human dental caries using high-resolution, large field of view synchrotron X-ray micro-computed tomography

3D analysis of enamel demineralisation in human dental caries using high-resolution, large field of view synchrotron X-ray micro-computed tomography

 

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

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Step-by-step guide to post-acquisition correlation of confocal and FIB/SEM volumes using Amira software

Step-by-step guide to post-acquisition correlation of confocal and FIB/SEM volumes using Amira software

In recent years new methodologies and workflow pipelines for acquiring correlated fluorescence microscopy and volume electron microscopy datasets have been extensively described and made accessible to users of different levels. Post-acquisition image processing, and particularly correlation of the optical and electron data in a single integrated three-dimensional framework can be key for extracting valuable information, especially when imaging large sample volumes such as whole cells or tissu... Read more

Allon Weiner

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The Spontaneous Emulsification of Entrained Inclusions During Casting of High Aluminum Steels

The Spontaneous Emulsification of Entrained Inclusions During Casting of High Aluminum Steels

The cleanliness of liquid steel is defined by the amounts of dissolved unwanted impurities and precipitated unwanted non-metallic phases.[…] Improving the cleanliness of the steel would mean a lower fraction of impurities in the final product. […] A novel approach, utilizing controlled synthetic inclusion/metal samples, has been developed to study the reactions between free inclusion-slag droplets and steel. The technique combines High-Temperature Confocal Scanning Laser Microscop... Read more

Akalya Raviraj, Nadia Kourra, Mark A. Williams, Gert Abbel, Claire Davis, Wouter Tiekink, Seetharaman Sridhar & Stephen Spooner

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Thermal Runaway of a Li-Ion Battery Studied by Combined ARC and Multi-Length Scale X-ray CT

Thermal Runaway of a Li-Ion Battery Studied by Combined ARC and Multi-Length Scale X-ray CT

Lithium ion battery failure occurs across multiple length scales. In this work, the properties of thermal failure and its effects on electrode materials were investigated in a commercial battery using a combination of accelerating rate calorimetry (ARC) and multi-length scale X-ray computed tomography (CT). ARC measured the heat dissipated from the cell during thermal runaway and enabled the identification of key thermal failure characteristics such as onset temperature and the rate of heat g... Read more

Drasti Patel, James B. Robinson, Sarah Ball, Daniel J. L. Brett and Paul R. Shearing

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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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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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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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