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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Fast and precise targeting of single tumor cells in vivo by multimodal correlative microscopy

Fast and precise targeting of single tumor cells in vivo by multimodal correlative microscopy

Intravital microscopy provides dynamic understanding of multiple cell biological processes, but its limited resolution has so far precluded structural analysis. Because it is difficult to capture rare and transient events, only a few attempts have been made to observe specific developmental and pathological processes in animal models using electron microscopy. The multimodal correlative approach that we propose here combines intravital microscopy, microscopic X-ray computed tomography and thr... Read more

Matthia A. Karreman, Luc Mercier, Nicole L. Schieber, Gergely Solecki, Guillaume Allio, Frank Winkler, Bernhard Ruthensteiner, Jacky G. Goetz, Yannick Schwab

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High-resolution structures of HIV-1 Gag cleavage mutants determine structural switch for virus maturation

High-resolution structures of HIV-1 Gag cleavage mutants determine structural switch for virus maturation

HIV-1 maturation occurs via multiple proteolytic cleavages of the Gag polyprotein, causing rearrangement of the virus particle required for infectivity. (…) How individual cleavages contribute to changes in protein structure and interactions, and how the mature, conical capsid forms, are poorly understood. Here, we employed cryoelectron tomography to determine morphology and high-resolution CA lattice structures for HIV1 derivatives in which Gag cleavage sites are mutated. These analyse... Read more

Simone Mattei, Aaron Tan, Barbel Glass, Barbara Muller, Hans-Georg Krausslich, and John A. G. Briggs

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Ultrastructural Characterization of Flashing Mitochondria

Ultrastructural Characterization of Flashing Mitochondria

Mitochondria undergo spontaneous transient elevations in matrix pH associated with drops in mitochondrial membrane potential. These mitopHlashes require a functional respiratory chain and the profusion protein optic atrophy 1, but their mechanistic basis is unclear. To gain insight on the origin of these dynamic events, we resolved the ultrastructure of flashing mitochondria by correlative light and electron microscopy. HeLa cells expressing the matrix-targeted pH probe mitoSypHer were screen... Read more

Manon Rosselin, Paula Nunes-Hasler, and Nicolas Demaurex

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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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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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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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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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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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Cell-type specific innervation of cortical pyramidal cells at their apical tufts

Cell-type specific innervation of cortical pyramidal cells at their apical tufts

We investigated the synaptic innervation of apical tufts of cortical pyramidal cells in a region between layers 1 and 2 using 3-D electron microscopy (3D-EM) applied to four cortical regions in mouse. Across all cortices, we found the relative inhibitory input at the apical dendrite’s main bifurcation to be more than 3-fold stronger for layer 2 pyramidal cells than for all other pyramidal cells. Towards the distal tuft dendrites in upper layer 1, however, the relative inhibitory input was a... Read more

Ali Karimi, Jan Odenthal, Florian Drawitsch, Kevin M. Boergens, Moritz Helmstaedter

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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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Morphological process of podocyte development revealed by block-face scanning electron microscopy

Morphological process of podocyte development revealed by block-face scanning electron microscopy

Podocytes present a unique 3D architecture specialized for glomerular filtration. However, several 3D morphological aspects on podocyte development remain partially understood because they are difficult to reveal using conventional scanning electron microscopy (SEM). Here, we adopted serial block-face SEM imaging…

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Koichiro Ichimura, Soichiro Kakuta, Yuto Kawasaki, Takayuki Miyaki, Takahiro Nonami, Naoyuki Miyazaki, Tomoyo Nakao, Sakiko Enomoto, Shigeo Arai, Masato Koike, Kazuyoshi Murata, Tatsuo Sakai

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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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A global approach for quantitative super resolution and electron microscopy on cryo and epoxy sections using self-labeling protein tags

A global approach for quantitative super resolution and electron microscopy on cryo and epoxy sections using self-labeling protein tags

Correlative light and electron microscopy (CLEM) is a powerful approach to investigate the molecular ultrastructure of labeled cell compartments. However, quantitative CLEM studies are rare, mainly due to small sample sizes and the sensitivity of fluorescent proteins to strong fixatives and contrasting reagents for EM. Here, we show that fusion of…

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Andreas Müller, Martin Neukam, Anna Ivanova, Anke Sönmez, Carla Münster, Susanne Kretschmar, Yannis Kalaidzidis, Thomas Kurth, Jean-Marc Verbavatz & Michele Solimena

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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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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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Juvenile Ovine Ex Vivo Larynges: Phonatory, Histologic, and Micro CT Based Anatomic Analyses

Juvenile Ovine Ex Vivo Larynges: Phonatory, Histologic, and Micro CT Based Anatomic Analyses

It is well known that the phonatory process changes during the life span. However, detailed investigations on potential factors concerned are rare. To deal with this issue, we performed extended biomechanical, macro anatomical, and histological analyses of the contributing laryngeal structures in ex vivo juvenile sheep models. Altogether twelve juvenile sheep larynges were analyzed within the phonatory experiments. Three different elongation levels and 16 different flow levels were applied to... Read more

Michael Döllinger, Olaf Wendler, Claus Gerstenberger, Tanja Grossmann, Marion Semmler, Hossein Sadeghi, and Markus Gugatschka

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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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Intrinsic dynamics study identifies two amino acids of TIMP-1 critical for its LRP-1-mediated endocytosis in neurons

Intrinsic dynamics study identifies two amino acids of TIMP-1 critical for its LRP-1-mediated endocytosis in neurons

The tissue inhibitor of metalloproteinases-1 (TIMP-1) exerts inhibitory activity against matrix metalloproteinases and cytokine-like effects. We previously showed that TIMP-1 reduces neurite outgrowth in mouse cortical neurons and that this cytokine-like effect depends on TIMP-1 endocytosis mediated by the low-density lipoprotein receptor-related protein-1 (LRP-1). To gain insight into the interaction between TIMP-1 and LRP-1, we considered conformational changes that occur when a ligand bind... Read more

Laurie Verzeaux, Nicolas Belloy, Jessica Thevenard-Devy, Jérôme Devy, Géraldine Ferracci, Laurent Martiny, Stéphane Dedieu, Manuel Dauchez, Hervé Emonard, Nicolas Etique & Emmanuelle Devarenne-Charpentier

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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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3D Muscle Architecture of the Pectoral Muscles of European Starling (Sturnus vulgaris)

3D Muscle Architecture of the Pectoral Muscles of European Starling (Sturnus vulgaris)

Avian flight is achieved through a number of modifications to the body, including the pectoral girdle (…). Muscle architecture is a critical variable in determining the biomechanical function of the vertebrate musculoskeletal system; however, accurate three-dimensional (3D) understanding of muscle architecture has been historically difficult to acquire. Here, we present a musculoskeletal model of a European starling (Sturnus vulgaris) pectoral girdle generated from iodine contr... Read more

S.P. Sullivan, F.R. McGechie, K.M. Middleton, C.M. Holliday

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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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