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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Preclinical Evaluation of 203/212Pb-Labeled Low-Molecular-Weight Compounds for Targeted Radiopharmaceutical Therapy of Prostate Cancer

Preclinical Evaluation of 203/212Pb-Labeled Low-Molecular-Weight Compounds for Targeted Radiopharmaceutical Therapy of Prostate Cancer

Targeted radiopharmaceutical therapy (TRT) using α-particle radiation is a promising approach for treating both large and micrometastatic lesions. Researchers developed prostate-specific membrane antigen (PSMA)–targeted low-molecular-weight agents for 212Pb-based TRT of patients with prostate cancer (PC) by evaluating the matching γ-emitting surrogate.

Targeted radiopharmaceutical therapy using α-particles (α-TRTs), which cause deposition of ionizing radiation of high-linear-ener... Read more

Sangeeta Ray Banerjee, Il Minn, Vivek Kumar, Anders Josefsson, Ala Lisok, Mary Brummet, Jian Chen, Ana P. Kiess, Kwamena Baidoo, Cory Brayton, Ronnie C. Mease, Martin Brechbiel, George Sgouros, Robert F. Hobbs, and Martin G. Pomper

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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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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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3D electron tomography of brain tissue unveils distinct Golgi structures that sequester cytoplasmic contents in neurons

3D electron tomography of brain tissue unveils distinct Golgi structures that sequester cytoplasmic contents in neurons

Macroautophagy is morphologically characterized by autophagosome formation. Autophagosomes are double-membraned vesicles that sequester cytoplasmic components for further degradation in the lysosome. Basal autophagy is paramount for intracellular quality control in post-mitotic cells but, surprisingly, the number of autophagosomes in post-mitotic neurons is very low, suggesting that alternative degradative structures could exist in neurons…

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Maria Rosario Fernandez-Fernandez, Desire Ruiz-Garcia, Eva Martin-Solana, Francisco Javier Chichon, Jose L. Carrascosa, Jose-Jesus Fernandez

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Collagen-Based Matrices for Osteoconduction: A Preclinical In Vivo Study

Collagen-Based Matrices for Osteoconduction: A Preclinical In Vivo Study

The aim of this study was to evaluate the influence of additional hydroxyapatite (HA) in collagen-based matrices (CM) and membrane placement on bone formation in calvarial defects.

Critical size defects in the calvaria of 16 New Zealand White Rabbits were randomly treated with CM or mineralized collagen-based matrices (mCM). Half of the sites were covered with a collagen membrane. Animals were euthanized after 12 weeks of healing. The samples were studied by micro-CT and histology. New... Read more

Hiroki Katagiri, Yacine El Tawil, Niklaus P. Lang, Jean-Claude Imber, Anton Sculean, Masako Fujioka-Kobayashi and Nikola Saulacic

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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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Multiple membrane extrusion sites drive megakaryocyte migration into bone marrow blood vessels

Multiple membrane extrusion sites drive megakaryocyte migration into bone marrow blood vessels

Platelets, cells central to hemostasis and thrombosis, are formed from parent cell megakaryocytes. Although the process is highly efficient in vivo, our ability to generate them in vitro is still remarkably inefficient. We proposed that greater understanding of the process in vivo is needed and used an imaging approach, intravital correlative light electron microscopy, to visualize platelet generation in bone marrow in the living mouse. In contrast to current understanding, we found that most... Read more

Edward Brown, Leo M Carlin, Claus Nerlov, Cristina Lo Celso, Alastair W Poole

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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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3D Dissection of Structural Membrane-Wall Contacts in Filamentous Moss Protonemata

3D Dissection of Structural Membrane-Wall Contacts in Filamentous Moss Protonemata

Cell-to-cell contact is essential for communication and development of multicellular organisms. A prerequisite is the passage through membranes. That way, molecular exchange and information flow is regulated via hormones, membrane proteins and pores.
In plants, the rigid cell walls prevent large membrane contact areas between protoplasts. Only plasmodesmata, minute channels between adjacent cells, form direct connections. Often, molecular data of the proteins involved are manifold but t... Read more

Dominik Harant and Ingeborg Lang

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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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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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SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography

SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID19 pandemic, is a highly pathogenic β-coronavirus. As other coronaviruses, SARS-CoV-2 is enveloped, replicates in the cytoplasm and assembles at intracellular membranes. Here, we structurally characterize the viral replication compartment and report critical insights into the budding mechanism of the virus, and the structure of extracellular virions close to their native state by in situ cryo-electr... Read more

Steffen Klein, Mirko Cortese, Sophie L. Winter, Moritz Wachsmuth-Melm, Christopher J. Neufeldt, Berati Cerikan, Megan L. Stanifer, Steeve Boulant, Ralf Bartenschlager, Petr Chlanda

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Differentiation and Characterization of Excitatory and Inhibitory Synapses by Cryo-electron Tomography and Correlative Microscopy

Differentiation and Characterization of Excitatory and Inhibitory Synapses by Cryo-electron Tomography and Correlative Microscopy

As key functional units in neural circuits, different types of neuronal synapses play distinct roles in brain information processing, learning, and memory. Synaptic abnormalities are believed to underlie various neurological and psychiatric disorders. Here, by combining cryo-electron tomography and cryo-correlative light and electron microscopy, we distinguished intact excitatory and inhibitory synapses of cultured hippocampal neurons, and visualized the in situ 3D organization of ... Read more

Chang-Lu Tao, Yun-Tao Liu, Rong Sun, Bin Zhang, Lei Qi, Sakar Shivakoti, Chong-Li Tian, Peijun Zhang, Pak-Ming Lau, Z. Hong Zhou and Guo-Qiang Bi

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Cerebral Corpora amylacea are dense membranous labyrinths containing structurally preserved cell organelles

Cerebral Corpora amylacea are dense membranous labyrinths containing structurally preserved cell organelles

Corpora amylacea are cell-derived structures that appear physiologically in the aged human brain. While their histological identification is straightforward, their ultrastructural composition and microenvironment at the nanoscale have remained unclear so far, as has their relevance to aging and certain disease states that involve the sequestration of toxic cellular metabolites. Here, we apply correlative serial block-face scanning electron microscopy and transmission electron tomograp... Read more

Paula P. Navarro, Christel Genoud, Daniel Castaño-Díez, Alexandra Graff-Meyer, Amanda J. Lewis, Yvonne de Gier, Matthias E. Lauer, Markus Britschgi, Bernd Bohrmann, Stephan Frank, Jürgen Hench, Gabriel Schweighauser, Annemieke J. M. Rozemuller, Wilma D. J. van de Berg, Henning Stahlberg & Sarah H. Shahmoradian

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Novel Sulfolobus Virus with an Exceptional Capsid Architecture

Novel Sulfolobus Virus with an Exceptional Capsid Architecture

A novel archaeal virus, denoted Sulfolobus ellipsoid virus 1 (SEV1), was isolated from an acidic hot spring in Costa Rica. The morphologically unique virion of SEV1 contains a protein capsid with 16 regularly spaced striations and an 11-nm-thick envelope. The capsid exhibits an unusual architecture in which the viral DNA, probably in the form of a nucleoprotein filament, wraps around the longitudinal axis of the virion in... Read more

Haina Wang, Zhenqian Guo, Hongli Feng, Yufei Chen, Xiuqiang Chen, Zhimeng Li, Walter Hernández-Ascencio, Xin Dai, Zhenfeng Zhang, Xiaowei Zheng, Marielos Mora-López, Yu Fu, Chuanlun Zhang, Ping Zhu, Li Huang

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Determining the bacterial cell biology of planctomycetes

Determining the bacterial cell biology of planctomycetes

Bacteria of the phylum Planctomycetes have been previously reported to possess several features that are typical of eukaryotes, such as cytosolic compartmentalization and endocytosis-like macromolecule uptake. However, recent evidence points towards a Gram-negative cell plan for Planctomycetes, although in-depth experimental analysis has been hampered by insufficient genetic tools…

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Christian Boedeker, Margarete Schüler, Greta Reintjes, Olga Jeske, Muriel C. F. van Teeseling et al.

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Three-dimensional imaging of the intracellular assembly of a functional viral RNA replicase complex

Three-dimensional imaging of the intracellular assembly of a functional viral RNA replicase complex

Positive-strand RNA viruses, which can be devastating pathogens in humans, animals and plants, replicate their genomes on intracellular membranes. Here, we describe the three-dimensional ultrastructural organization of a tombusvirus replicase in yeast, a valuable model for exploring virus–host interactions…

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Isabel Fernández de Castro, José J. Fernández, Daniel Barajas, Peter D. Nagy, Cristina Risco

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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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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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