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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Organism motility in an oxygenated shallow-marine environment 2.1 billion years ago

Organism motility in an oxygenated shallow-marine environment 2.1 billion years ago

Evidence for macroscopic life in the Paleoproterozoic Era comes from 1.8 billion-year-old (Ga) compression fossils [Han TM, Runnegar B (1992) Science 257:232–235; Knoll et al. (2006) Philos Trans R Soc Lond B 361:1023–1038],  Stirling biota [Bengtson S et al. (2007) Paleobiology 33:351–381], and large colonial organisms exhibiting signs of coordinated growth from the 2.1-Ga Francevillian series, Gabon. Here we report on pyritized string-shaped structures from... Read more

Abderrazak El Albani, M. Gabriela Mangano, Luis A. Buatois, Stefan Bengtson, Armelle Riboulleau, Andrey Bekker, Kurt Konhauser, Timothy Lyons, Claire Rollion-Bard, Olabode Bankole, Stellina Gwenaelle Lekele Baghekema, Alain Meunier, Alain Trentesaux, Arnaud Mazurier, Jeremie Aubineau, Claude Laforest, Claude Fontaine, Philippe Recourt, Ernest Chi Fru, Roberto Macchiarelli, Jean Yves Reynaud, François Gauthier-Lafaye, and Donald E. Canfield

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UCSF School of Dentistry uses Avizo software to extract changes in periodontal ligament space and tooth movement due to orthodontic therapy

UCSF School of Dentistry uses Avizo software to extract changes in periodontal ligament space and tooth movement due to orthodontic therapy

During the acts of biting and chewing, the muscles of the jaw (consisting of the masseter, temporalis, and medial pterygoid in the elevator group, and lateral pterygoid as the main depressor) generate forces that dictate jaw kinematics . The movement of jaws hinges about the temporomandibular joint and are brought together by the muscles attached to respective bones through bone-tendon interfaces known as entheses . Thus, chewing forces affect aspects of craniofacial structure as well as bo... Read more

Kyle H.-Y. Chan, fourth-year undergraduate student in Molecular and Cell Biology, and Public Health at UC Berkeley, FeiFei Yang, Ph.D., postdoctoral scholar in the Laboratory of Multiscale Biomechanics and Biomineralization, School of Dentistry, UCSF, and Sunita P. Ho, Ph.D., Division of Biomaterials and Bioengineering, Department of Preventive and Restorative Dental Sciences, School of Dentistry, University of California San Francisco

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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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2 BILLION years old fossils appear to represent a first experiment in megascopic multicellularity

2 BILLION years old fossils appear to represent a first experiment in megascopic multicellularity

The Paleoproterozoic Era witnessed crucial steps in the evolution of Earth’s surface environments following the first appreciable rise of free atmospheric oxygen concentrations ∼2.3 to 2.1 Ga ago, and concomitant shallow ocean oxygenation. Combined microtomography, geochemistry, and sedimentary analysis suggest a biota fossilized during early diagenesis. The emergence of this biota follows a rise in atmospheric oxygen, which is consistent with the idea that surface oxygenation allowe... Read more

Abderrazak El Albani, Laboratoire HYDRASA, UMR 6269 CNRS-INSU, Université de Poitiers, France

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Influence of Deformation and Stress between Bone and Implant from Various Bite Forces by Numerical Simulation Analysis

Influence of Deformation and Stress between Bone and Implant from Various Bite Forces by Numerical Simulation Analysis

Endosseous oral implant is applied for orthodontic anchorage in subjects with multiple tooth agenesis. Its effectiveness under orthodontic loading has been demonstrated clinically and experimentally. This study investigates the deformation and stress on the bone and implant for different bite forces by three-dimensional (3D) finite element (FE) methods. A numerical simulation of deformation and stress distributions around implants was used to estimate the survival life for implants. The model... Read more

Hsin-Chung Cheng, Boe-Yu Peng, May-Show Chen, Chiung-Fang Huang, Yi Lin, and Yung-Kang Shen

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C. elegans chromosomes connect to centrosomes by anchoring into the spindle network

C. elegans chromosomes connect to centrosomes by anchoring into the spindle network

The mitotic spindle ensures the faithful segregation of chromosomes. Here we combine the first large-scale serial electron tomography of whole mitotic spindles in early C. elegans embryos with live-cell imaging to reconstruct all microtubules in 3D and identify their plus- and minus-ends. We classify them as kinetochore (KMTs), spindle (SMTs) or astral microtubules (AMTs) according to their positions, and quantify distinct properties of each class. While our light microscopy and muta... Read more

Stefanie Redemann, Johannes Baumgart, Norbert Lindow, Michael Shelley, Ehssan Nazockdast, Andrea Kratz, Steffen Prohaska, Jan Brugués, Sebastian Fürthauer & Thomas Müller-Reichert

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Modernization of Golgi staining techniques for high-resolution, 3-dimensional imaging of individual neurons

Modernization of Golgi staining techniques for high-resolution, 3-dimensional imaging of individual neurons

Analysis of neuronal arborization and connections is a powerful tool in fundamental and clinical neuroscience. Changes in neuronal morphology are central to brain development and plasticity and are associated with numerous diseases. Golgi staining is a classical technique based on a deposition of metal precipitate in a random set of neurons. Despite their versatility, Golgi methods have limitations that largely precluded their use in advanced microscopy. We combined Golgi staining with fluore... Read more

Katlijn Vints, Dorien Vandael, Pieter Baatsen, Benjamin Pavie, Frank Vernaillen, Nikky Corthout, Vasily Rybakin, Sebastian Munck & Natalia V. Gounko

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Correlative cryo-electron microscopy reveals the structure of TNTs in neuronal cells

Correlative cryo-electron microscopy reveals the structure of TNTs in neuronal cells

The orchestration of intercellular communication is essential for multicellular organisms. One mechanism by which cells communicate is through long, actin-rich membranous protrusions called tunneling nanotubes (TNTs), which allow the intercellular transport of various cargoes, between the cytoplasm of distant cells in vitro and in vivo. Here, we use correlative FIB-SEM, light- and cryo-electron microscopy approaches to elucidate the structural organization of neuronal TNTs. Our data indicate ... Read more

Anna Sartori-Rupp, Diégo Cordero Cervantes, Anna Pepe, Karine Gousset, Elise Delage, Simon Corroyer-Dulmont, Christine Schmitt, Jacomina Krijnse-Locker & Chiara Zurzolo

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Immunofluorescence Tomography: High-resolution 3-D reconstruction by serial-sectioning of methacrylate embedded tissues and alignment of 2-D immunofluorescence images

Immunofluorescence Tomography: High-resolution 3-D reconstruction by serial-sectioning of methacrylate embedded tissues and alignment of 2-D immunofluorescence images

Immunofluorescence tomography is a high-resolution 3-D reconstruction method based on methacrylate embedding and serial-sectioning, where 2-D images of immuno-stained serial-sections are computationally aligned into image stacks, and the 3-D volume rendered. Butyl-Methyl Methacrylate (BMMA) plastic was adopted as it preserves excellent tissue morphology and can be de-plasticized easily using an organic solvent, which enables immuno-staining of serial-sections without antibody penetration issu... Read more

Parfitt, Geraint J

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In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment

In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment

Protein aggregation and dysfunction of the ubiquitin-proteasome system are hallmarks of many neurodegenerative diseases. Here, we address the elusive link between these phenomena by employing cryo-electron tomography to dissect the molecular architecture of protein aggregates within intact neurons at high resolution. We focus on the poly-Gly-Ala (poly-GA) aggregates resulting from aberrant translation of an expanded GGGGCC repeat in C9orf72, the most common genetic cause of amyotrophic latera... Read more

Qiang Guo, Carina Lehmer, Antonio Martinez-Sanchez, Till Rudack, Florian Beck, Hannelore Hartmann, Manuela Perez-Berlanga, Frederic Frottin, Mark S.Hipp, F. Ulrich Hartl, Dieter Edbauer, Wolfgang Baumeister, Ruben Fernandez-Busnadiego

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The structure of the COPI coat determined within the cell

The structure of the COPI coat determined within the cell

COPI-coated vesicles mediate trafficking within the Golgi apparatus and from the Golgi to the endoplasmic reticulum. Here, we applied cryo-focused ion beam milling, cryo-electron tomography and subtomogram averaging to determine the native structure of the COPI coat within vitrified Chlamydomonas reinhardtii cells. The native algal structure resembles the in vitro mammalian structure, but additionally reveals cargo bound beneath beta’–COP. We find that all coat components disassemble... Read more

Yury S Bykov, Miroslava Schaffer, Svetlana O Dodonova, Sahradha Albert, Jurgen M Plitzko, Wolfgang Baumeister, Benjamin D Engel, John AG Briggs

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Biological serial block face scanning electron microscopy at improved z-resolution based on Monte Carlo model

Biological serial block face scanning electron microscopy at improved z-resolution based on Monte Carlo model

Serial block-face electron microscopy (SBEM) provides nanoscale 3D ultrastructure of embedded and stained cells and tissues in volumes of up to 107 µm3. In SBEM, electrons with 1–3 keV energies are incident on a specimen block, from which backscattered electron (BSE) images are collected with xy resolution of 5–10 nm in the block-face plane, and successive layers are removed by an in situ ultramicrotome. Sp... Read more

Q. He, M. Hsueh, G. Zhang, D. C. Joy & R. D. Leapman

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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 FEI CorrSight with MAPS, have allowed for a more reliable, reproducible, and quicker approach to correlate three-dimensional time-lapse confocal fluo... 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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Full reconstruction of large lobula plate tangential cells in Drosophila from a 3D EM dataset

Full reconstruction of large lobula plate tangential cells in Drosophila from a 3D EM dataset

With the advent of neurogenetic methods, the neural basis of behavior is presently being analyzed in more and more detail. This is particularly true for visually driven behavior of Drosophila melanogaster where cell-specific driver lines exist that, depending on the combination with appropriate effector genes, allow for targeted recording, silencing and optogenetic stimulation of individual cell-types. Together with detailed connectomic data of large parts of the fly optic lobe, this has rece... Read more

Kevin M. Boergens , Christoph Kapfer, Moritz Helmstaedter, Winfried Denk, Alexander Borst

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Investigation of Hot Pressed Polymer Electrolyte Fuel Cell Assemblies via Xray Computed Tomography

Investigation of Hot Pressed Polymer Electrolyte Fuel Cell Assemblies via Xray Computed Tomography

The hot pressing process for fabricating membrane electrode assemblies (MEAs) has been widely adopted, yet little is known of its effects on the microstructural properties of the different components of the MEA. In particular, the interaction of the electrolyte, electrode and gas diffusion layer (GDL) due to lamination is difficult to probe as conventional imaging techniques cannot access the internal structure of the MEA. Here, a novel approach is used, which combines characterisation of hot... Read more

Q. Meyer, N. Mansor, F. Iacoviello, P.L. Cullen, R. Jervis, D. Finegan, C. Tan, J. Bailey, P. R. Shearing, D. J. L. Brett

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The effect of wetting area in carbon paper electrode on the performance of vanadium redox flow batteries: A three-dimensional lattice Boltzmann study

The effect of wetting area in carbon paper electrode on the performance of vanadium redox flow batteries: A three-dimensional lattice Boltzmann study

The vanadium redox flow battery (VRFB) has emerged as a promising technology for large-scale storage of intermittent power generated from renewable energy sources due to its advantages such as scalability, high energy efficiency and low cost. In the current study, a three-dimensional(3D) Lattice Boltzmann model is developed to simulate the transport mechanisms of electrolyte flow, species and charge in the vanadium redox flow battery at the micro pore scale. An electrochemical model using the... Read more

Duo Zhang, Qiong Cai, Oluwadamilola O.Taiwo, Vladimir Yufit, Nigel P.Brandon, Sai Gu

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High-resolution ultramicroscopy of the developing and adult nervous system in optically cleared Drosophila melanogaster

High-resolution ultramicroscopy of the developing and adult nervous system in optically cleared Drosophila melanogaster

The fruit fly, Drosophila melanogaster, is an important experimental model to address central questions in neuroscience at an organismic level. However, imaging of neural circuits in intact fruit flies is limited due to structural properties of the cuticle. Here we present a novel approach combining tissue clearing, ultramicroscopy, and data analysis that enables the visualisation of neuronal networks with single-cell resolution from the larval stage up to the adult Drosophila. (…) This... Read more

Marko Pende, Klaus Becker, Martina Wanis, Saiedeh Saghafi, Rashmit Kaur, Christian Hahn, Nika Pende, Massih Foroughipour, Thomas Hummel & Hans-Ulrich Dodt

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Autophagy Proteins Promote Repair of Endosomal Membranes Damaged by the Salmonella Type Three Secretion System 1

Autophagy Proteins Promote Repair of Endosomal Membranes Damaged by the Salmonella Type Three Secretion System 1

Salmonella Typhimurium (S.Tm) is an enteropathogen requiring multiple virulence factors, including two type three secretion systems (T1 and T2). T1 triggers epithelium invasion in which the bacteria are taken up into endosomes that mature into Salmonella-containing vacuoles (SCV) and trigger T2 induction upon acidification. Mechanisms controlling endosome membrane integrity or pathogen egress into the cytosol are incompletely understood. We screened for host factors affecting invasion and SCV... Read more

Saskia Kreibich, Mario Emmenlauer, Jennifer Fredlund, Pauli Rämö, Christian Münz, Christoph Dehio, Jost Enninga, Wolf-Dietrich Hardt

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Loss of adult skeletal muscle stem cells drives age-related neuromuscular junction degeneration

Loss of adult skeletal muscle stem cells drives age-related neuromuscular junction degeneration

Neuromuscular junction degeneration is a prominent aspect of sarcopenia, the age-associated loss of skeletal muscle integrity. Previously, we showed that muscle stem cells activate and contribute to mouse neuromuscular junction regeneration in response to denervation (Liu et al., 2015). Here, we examined gene expression profiles and neuromuscular junction integrity in aged mouse muscles, and unexpectedly found limited denervation despite a high level of degenerated neuromuscular junctions. In... Read more

Wenxuan Liu, Alanna Klose, Sophie Forman, Nicole D Paris, Lan Wei-LaPierre, Mariela Cortés-Lopéz, Aidi Tan, Morgan Flaherty, Pedro Miura, Robert T Dirksen, Joe V Chakkalakal

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Investigation of pressure drop in 3D replicated open-cell foams: Coupling CFD with experimental data on additively manufactured foams

Investigation of pressure drop in 3D replicated open-cell foams: Coupling CFD with experimental data on additively manufactured foams

Open-cell foams as structured catalyst supports are promising candidates for the design of high throughput catalytic processes. In this contribution, we employ a coupled numerical and experimental approach to assess the pressure losses in foams. (…) we explore virtually-generated foam models and their 3D printed replicas for a combined CFD and experimental study of fluid dynamics in foams. In particular, we focus our analysis on the low Reynolds number regime, where deviations between t... Read more

Mauro Bracconi, Matteo Ambrosetti, Obinna Okafor, Victor Sans, Xun Zhang, Xiaoxia Ou, Claudio Pereira Da Fonte, Xiaolei Fan, Matteo Maestri, Gianpiero Groppi, Enrico Tronconi

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Vascular structure of the earliest shark teeth

Vascular structure of the earliest shark teeth

Here we use synchrotron tomography to characterise dental vasculature in the oldest known tooth-bearing sharks, Leonodus carlsi Mader, 1986 and Celtiberina maderi Wang, 1993. Three dimensional reconstruction of the vascular system and microstructure of both taxa revealed a complex and dense network of canals, including horizontal, ascending and secondary bifurcated canals, as well as histological features consistent with an osteodont histotype. However, L. carlsi and C. maderi also exhibit si... Read more

Carlos Martinez-Perez, Alba Martin-Lazaro, Humberto G Ferron, Martina Kirstein, Philip C.J. Donoghue, Hector Botella

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