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.

Use the Domain selector to filter by main application area, and use the Search box to enter keywords related to specific topics you are interested in.

Operando Visualization and Multi-scale Tomography Studies of Dendrite Formation and Dissolution in Zinc Batteries

Operando Visualization and Multi-scale Tomography Studies of Dendrite Formation and Dissolution in Zinc Batteries

Alternative battery technologies are required to meet growing energy demands and address the limitations of present technologies. As such, it is necessary to look beyond lithium-ion batteries. Zinc batteries enable high power density while being sourced from ubiquitous and cost-effective materials. This paper presents, for the first time known to the authors, multi-length scale tomography studies of failure mechanisms in zinc batteries with and without commercial microporous separators. In bo... Read more

Vladimir Yufit, Farid Tariq David S. Eastwood Moshiel Biton Billy Wu Peter D. Lee Nigel P. Brandon

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Microstructural analysis of TRISO particles using multi-scale X-ray computed tomography

Microstructural analysis of TRISO particles using multi-scale X-ray computed tomography

TRISO particles, a composite nuclear fuel built up by ceramic and graphitic layers, have outstanding high temperature resistance. TRISO fuel is the key technology for High Temperature Reactors (HTRs) and the Generation IV Very High Temperature Reactor (VHTR) variant.

TRISO offers unparalleled containment of fission products and is extremely robust during accident conditions. An understanding of the thermal performance and mechanical properties of TRISO fuel requires a detailed knowledg... Read more

T. Lowe, R.S. Bradley, S. Yue, K. Barii, J. Gelb, N. Rohbeck, J. Turner, P.J. Withers

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Label-free 3D-CLEM using endogenous tissue landmarks

Label-free 3D-CLEM using endogenous tissue landmarks

We demonstrate feasibility of the workflow by combining in vivo 2-photon microscopy and focused ion beam scanning electron microscopy (FIB/SEM) to dissect the role of astrocytic coverage in the persistence of dendritic spines.

Emerging 3D correlative light and electron microscopy (CLEM) approaches enable studying neuronal structure-function relations at unprecedented depth and precision. However, established protocols for the correlation of light and electron micrographs rely ... Read more

Manja Luckner,Steffen Burgold, Severin Filser, Maximilian Scheungrab, Yilmaz Niyaz, Eric Hummel, Gerhard Wanner, Jochen Herms

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A fully integrated, three-dimensional fluorescence to electron microscopy correlative workflow

A fully integrated, three-dimensional fluorescence to electron microscopy correlative workflow

While fluorescence microscopy provides tools for highly specific labeling and sensitive detection, its resolution limit and lack of general contrast has hindered studies of cellular structure and protein localization. Recent advances in correlative light and electron microscopy (CLEM), including the fully integrated CLEM workflow instrument, the Thermo Scientific CorrSight with MAPS, have allowed for a more reliable, reproducible, and quicker approach to correlate three-dimensional time-lapse... Read more

Claudia S. Lopez, Cedric Bouchet-Marquis, Christopher P. Arthur, Jessica L. Riesterer, Gregor Heiss, Guillaume Thibault, Lee Pullan, Sunjong Kwon, Joe W. Gray

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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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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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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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Ovipositor of the braconid wasp Habrobracon hebetor: structural and functional aspects

Ovipositor of the braconid wasp Habrobracon hebetor: structural and functional aspects

The Braconidae are a megadiverse and ecologically highly important group of insects. The vast majority of braconid wasps are parasitoids of other insects, usually attacking the egg or larval stages of their hosts. The ovipositor plays a crucial role in the assessment of the potential host and precise egg laying. We used lightand electron-microscopic techniques to investigate all inherent cuticular elements of the ovipositor (the female 9th abdominal tergum, two pairs of valvifers, and three p... Read more

Michael Csader, Karin Mayer, Oliver Betz, Stefan Fischer, Benjamin Eggs

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A high-throughput semi-automated bone segmentation workflow for murine hindpaw Micro-CT datasets

A high-throughput semi-automated bone segmentation workflow for murine hindpaw Micro-CT datasets

Micro-computed tomography (μCT) is a valuable imaging modality for longitudinal quantification of bone volumes to identify disease or treatment effects for a broad range of conditions that affect bone health. Complex structures, such as the hindpaw with up to 31 distinct bones in mice, have considerable analytic potential, but quantification is often limited to a single bone volume metric due to the intensive effort of manual segmentation. Herein, we introduce a high-throughput, user-friendl... Read more

H. Mark Kenney, Yue Peng, Kiana L.Chen, Raquel Ajalik, Lindsay Schnur, Ronald W.Wood, Edward M.Schwarz, Hani A. Awad

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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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Optical tissue clearing and machine learning can precisely characterize extravasation and blood vessel architecture in brain tumors

Optical tissue clearing and machine learning can precisely characterize extravasation and blood vessel architecture in brain tumors

Precise methods for quantifying drug accumulation in brain tissue are currently very limited, challenging the development of new therapeutics for brain disorders. Transcardial perfusion is instrumental for removing the intravascular fraction of an injected compound, thereby allowing for ex vivo assessment of extravasation into the brain. However, pathological remodeling of tissue microenvironment can affect the efficiency of transcardial perfusion, which has been largely overlooked.

We... Read more

Serhii Kostrikov, Kasper B. Johnsen, Thomas H. Braunstein, Johann M. Gudbergsson, Frederikke P. Fliedner, Elisabeth A. A. Obara, Petra Hamerlik, Anders E. Hansen, Andreas Kjaer, Casper Hempel & Thomas L. Andresen

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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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Patient-specific anatomical model for deep brain stimulation based on 7 Tesla MRI

Patient-specific anatomical model for deep brain stimulation based on 7 Tesla MRI

Deep brain stimulation (DBS) requires accurate localization of the anatomical target structure, and the precise placement of the DBS electrode within it. Ultra-high field 7 Tesla (T) MR images can be utilized to create patient-specific anatomical 3D models of the subthalamic nuclei (STN) to enhance pre-surgical DBS targeting as well as post-surgical visualization of the DBS lead position and orientation. We validated the accuracy of the 7T imaging-based patient-specific model of the STN and m... Read more

Yuval Duchin, Reuben R. Shamir, Remi Patriat, Jinyoung Kim, Jerrold L. Vitek, Guillermo Sapiro, Noam Harel

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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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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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Morphology of mitochondria in spatially restricted axons revealed by cryo-electron tomography

Morphology of mitochondria in spatially restricted axons revealed by cryo-electron tomography

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

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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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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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