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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Deep nuclear invaginations are linked to cytoskeletal filaments – integrated bioimaging of epithelial cells in 3D culture

Deep nuclear invaginations are linked to cytoskeletal filaments – integrated bioimaging of epithelial cells in 3D culture

The importance of context in regulation of gene expression is now an accepted principle; yet the mechanism by which the microenvironment communicates with the nucleus and chromatin in healthy tissues is poorly understood. A functional role for nuclear and cytoskeletal architecture is suggested by the phenotypic differences observed between epithelial and mesenchymal cells…

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Danielle M. Jorgens, Jamie L. Inman, Michal Wojcik, Claire Robertson, Hildur Palsdottir, Wen-Ting Tsai, Haina Huang, Alexandre Bruni-Cardoso, Claudia S. López, Mina J. Bissell, Ke Xu, Manfred Auer

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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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Patterns of organelle ontogeny through a cell cycle revealed by whole-cell reconstructions using 3D electron microscopy

Patterns of organelle ontogeny through a cell cycle revealed by whole-cell reconstructions using 3D electron microscopy

The major mammalian bloodstream form of the African sleeping sickness parasite Trypanosoma bruceimultiplies rapidly, and it is important to understand how these cells divide. Organelle inheritance involves complex spatiotemporal re-arrangements to ensure correct distribution to daughter cells…

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Louise Hughes, Samantha Borrett, Katie Towers, Tobias Starborg, Sue Vaughan

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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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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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Testing hypotheses for the function of the carnivoran baculum using finite-element analysis

Testing hypotheses for the function of the carnivoran baculum using finite-element analysis

The baculum (os penis) is a mineralized bone within the glans of the mammalian penis and is one of the most morphologically diverse structures in the mammal skeleton. (…) For the first time, to our knowledge, we apply a computational simulation approach (finite-element analysis; FEA) to quantify the three-dimensional biomechanical performance of carnivoran bacula (n = 74) based upon high-resolution micro-computed tomography scans. (…) a highly significant negative relation... Read more

Charlotte A. Brassey, James D. Gardiner, and Andrew C. Kitchener

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Comparative Morphology of the Internal Nasal Skeleton of Adult Marsupials Based on X-ray Computed Tomography

Comparative Morphology of the Internal Nasal Skeleton of Adult Marsupials Based on X-ray Computed Tomography

The internal skeleton of the nasal cavity is sporadically and often incompletely described for many marsupial species and mammals in general. Here, I provide an anatomical survey of the ethmoid in the skulls of adult marsupials based on examination of computed tomography (CT) imagery of 29 taxa representing all the major extant groups of marsupials. (…) I compared ecological data with the number of ecto- and endoturbinals as a preliminary test to determine whether some of the interspec... Read more

Thomas E. Macrini

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New omomyoids (Euprimates, Mammalia) from the late Uintan of southern California, USA, and the question of the extinction of the Paromomyidae (Plesiadapiformes, Primates)

New omomyoids (Euprimates, Mammalia) from the late Uintan of southern California, USA, and the question of the extinction of the Paromomyidae (Plesiadapiformes, Primates)

Paromomyidae has been thought to represent the longest-lived group of stem primates (plesiadapiforms), extending from the early Paleocene to late Eocene. We analyzed primate material from the late-middle Eocene of southern California that had initially been ascribed to cf. Phenacolemur shifrae. This material falls at the lowest end of the size range for the family. The Californian specimens also exhibit several dental features that are atypical for paromomyids, such as a strong paraconid on t... Read more

Sergi López-Torres, Mary T. Silcox, and Patricia A. Holroyd

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Mechanical adaptation of trabecular bone morphology in the mammalian mandible

Mechanical adaptation of trabecular bone morphology in the mammalian mandible

Alveolar bone, together with the underlying trabecular bone, fulfils an important role in providing structural support against masticatory forces. Diseases such as osteoporosis or periodontitis cause alveolar bone resorption which weakens this structural support and is a major cause of tooth loss. However, the functional relationship between alveolar bone remodelling within the molar region and masticatory forces is not well understood. This study investigated this relationship by comparing m... Read more

Peter J. Watson, Laura C. Fitton, Carlo Meloro, Michael J. Fagan, Flora Gröning

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Analysis of Void Volume in Composite Electrode of All-solid-state Lithium-ion Battery Employing FIB-SEM and Union Operation Image Processing

Analysis of Void Volume in Composite Electrode of All-solid-state Lithium-ion Battery Employing FIB-SEM and Union Operation Image Processing

We had proposed an image-processing scheme using union operation suitable for extracting target features with hierarchical dimensions from the original data, and applied it to void analysis in a composite electrode of an all-solid-state lithium ion battery (LIB). Void analysis is very important in developing better composite electrodes for all-solid-state LIBs because internal voids should increase the interfacial resistance. Film formation of electrode-solid electrolyte composites by the aer... Read more

Yuta Yamamoto , Yasutoshi Iriyama, and Shunsuke Muto

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Cardiogenic Airflow in the Lung Revealed Using Synchrotron-Based Dynamic Lung Imaging

Cardiogenic Airflow in the Lung Revealed Using Synchrotron-Based Dynamic Lung Imaging

The beating heart is known to produce pressure and airflow oscillations in the lungs of mammals. This phenomenon is often disregarded as detailed measurement of its effects in the lung have hitherto not been possible. Previous studies have attempted to measure the effect of these oscillations on gas mixing. However, the results have proven inconclusive, due to the lack of a direct measurement tool capable of flow measurement throughout the entire bronchial tree. Here we present the first deta... Read more

Stephen Dubsky, Jordan Thurgood, Andreas Fouras, Bruce R. Thompson & Gregory J. Sheard

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