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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Protocols for Generating Surfaces and Measuring 3D Organelle Morphology Using Amira

Protocols for Generating Surfaces and Measuring 3D Organelle Morphology Using Amira

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.

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Automatic whole cell organelle segmentation in volumetric electron microscopy

Automatic whole cell organelle segmentation in volumetric electron microscopy

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

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Imaging Fibroblast Activation Protein Alpha Improves Diagnosis of Metastatic Prostate Cancer with Positron Emission Tomography

Imaging Fibroblast Activation Protein Alpha Improves Diagnosis of Metastatic Prostate Cancer with Positron Emission Tomography

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

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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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Distribution of Serotonin-Immunoreactive Neurons in the Brain and Gnathal Ganglion of Caterpillar Helicoverpa armigera

Distribution of Serotonin-Immunoreactive Neurons in the Brain and Gnathal Ganglion of Caterpillar Helicoverpa armigera

Serotonin (5-hydroxytryptamine, 5-HT) is an important biogenic amine that acts as a neural circuit modulator. It is widespread in the central nervous system of insects. However, little is known about the distribution of serotonin in the nervous system of the cotton bollworm Helicoverpa armigera. In the present study, we performed immunohistochemical experiments with anti-serotonin serum to examine the distribution of serotonin in the central nervous system of H. armigera larv... Read more

Qing-Bo Tang, Wei-Wei Song, Ya-Jun Chang, Gui-Ying Xie, Wen-Bo Chen* and Xin-Cheng Zhao

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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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Asymmetric Centriole Numbers at Spindle Poles Cause Chromosome Missegregation in Cancer

Asymmetric Centriole Numbers at Spindle Poles Cause Chromosome Missegregation in Cancer

Chromosomal instability is a hallmark of cancer and correlates with the presence of extra centrosomes, which originate from centriole overduplication.

Overduplicated centrioles lead to the formation of centriole rosettes, which mature into supernumerary centrosomes in the subsequent cell cycle. While extra centrosomes promote chromosome missegregation by clustering into pseudo-bipolar spindles, the contribution of centriole rosettes to chromosome missegregation is unknown. We us... Read more

Marco R.Cosenza, Anna Cazzola, Annik Rossberg, Nicole L. Schieber, Gleb Konotop, Elena Bausch, Alla Slynko, Tim Holland-Letz, Marc S.Raab, Taronish Dubash, Hanno Glimm, Sven Poppelreuther, Christel Herold-Mende, Yannick Schwab, Alwin Krämer

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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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Microstructure analysis and image-based modelling of face masks for COVID-19 virus protection

Microstructure analysis and image-based modelling of face masks for COVID-19 virus protection

Until March 2021, around 120 million coronavirus disease (COVID-19) infected cases and over 2.6 million deaths have been reported worldwide. […] Recent investigations have implied that face masks help to reduce the disease transmission and therefore slow down the growth of the epidemic curve. However, there are still ongoing debates on the efficacy of wearing masks […] since there is a general lack of information relating to the material structure of commonly used face masks.Read more

Wenjia Du, Francesco Iacoviello, Tacson Fernandez, Rui Loureiro, Daniel J. L. Brett & Paul R. Shearing

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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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Phase-contrast and dark-field imaging for the inspection of resin-rich areas and fiber orientation in non-crimp vacuum infusion carbon-fiber-reinforced polymers

Phase-contrast and dark-field imaging for the inspection of resin-rich areas and fiber orientation in non-crimp vacuum infusion carbon-fiber-reinforced polymers

The high strength at moderate weight in combination with superior corrosion and fatigue properties makes carbon-fiber-reinforced polymer (CFRP) an attractive material for lightweight applications in aerospace. Nonetheless, besides several benefits, CFRP components also bear significant risks like a low resistance to impact damage. […] In this work, we present a multimodal approach to three-dimensionally quantify and visualize fiber orientation and resin-rich areas in carbon-fiber-reinf... Read more

Jonathan Glinz, Jan Šleichrt, Daniel Kytýř, Santhosh Ayalur-Karunakaran, Simon Zabler, Johann Kastner & Sascha Senck

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Fibre misalignment and breakage in 3D printing of continuous carbon fibre reinforced thermoplastic composites

Fibre misalignment and breakage in 3D printing of continuous carbon fibre reinforced thermoplastic composites

Continuous carbon fibre-reinforced polymer (CCFRP) composites have been increasingly used in airframes and other high-end industrial products due to their superior mechanical properties such as high strength-weight and stiffness-weight ratios […] Additive manufacturing (also known as 3D printing) has shown potential to fabricate continuous fibre-reinforced composites with highly complex shapes in both 2D and 3D. Among them, Fused Filament Fabrication (FFF) 3D printing melts and deposits... Read more

Haoqi Zhang, Jiayun Chen, Dongmin Yang

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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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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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A virtual testing platform for filter materials and textile masks

A virtual testing platform for filter materials and textile masks

In order to provide the population with consistent and science-based advice on preferred materials for face masks, we are characterizing the microstructure of different materials using X-ray microfocus computed tomography (microCT), and we use these datasets to simulate the pressure drop (i.e. measure for breathability). We validate our measurements with physically measured filter efficiency and pressure drop, and in this way, we try to develop a “virtual testing platform” for the charac... Read more

The ContrasTTeam of Prof. dr. Greet Kerckhofs, UCLouvain and MTM

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Investigation on the Fiber Orientation Distributions and Their Influence on the Mechanical Property of the Co-Injection Molding Products

Investigation on the Fiber Orientation Distributions and Their Influence on the Mechanical Property of the Co-Injection Molding Products

In recent years, due to the rapid development of industrial lightweight technology, composite materials based on fiber reinforced plastics (FRP) have been widely used in the industry. However, the environmental impact of the FRPs is higher each year. To overcome this impact, co-injection molding could be one of the good solutions. But how to make the suitable control on the skin/core ratio and how to manage the glass fiber orientation features are still significant challenges. In this study, ... Read more

Chao-Tsai Huang, Xuan-Wei Chen, Wei-Wen Fu

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Tracking tendon fibers to their insertion – a 3D analysis of the Achilles tendon enthesis in mice

Tracking tendon fibers to their insertion – a 3D analysis of the Achilles tendon enthesis in mice

Tendon insertions to bone are heavily loaded transitions between soft and hard tissues. The fiber courses in the tendon have profound effects on the distribution of stress along and across the insertion. We tracked fibers of the Achilles tendon in mice in micro-computed tomographies and extracted virtual transversal sections. The fiber tracks and shapes were analyzed from a position in the free tendon to the insertion with regard to their mechanical consequences. The fiber number was found to... Read more

Julian Sartori, Heiko Stark

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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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