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 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.
Multicellular tumour spheroids are used as a culture model to reproduce the 3D architecture, proliferation gradient and cell interactions of a tumour micro-domain. However, their 3D characterization at the cell scale remains challenging due to size and cell density issues. In this study, we developed a methodology based on 3D light sheet fluorescence microscopy (LSFM) image analysis and convex hull calculation that allows characterizing the 3D shape and orientation of cell nuclei relative to ... Read more
Annaïck Desmaison, Ludivine Guillaume, Sarah Triclin, Pierre Weiss, Bernard Ducommun & Valérie Lobjois
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
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
Actin waves are dynamic supramolecular structures involved in cell migration, cytokinesis, adhesion, and neurogenesis. Although wave-like propagation of actin networks is a widespread phenomenon, the actin architecture underlying wave propagation remained unknown. In situ cryo-electron tomography of Dictyostelium cells unveils the wave architecture and provides evidence for wave progression by de novo actin nucleation. Subtomogram averaging reveals the structu... Read more
Marion Jasnin, Florian Beck, Mary Ecke, Yoshiyuki Fukuda, Antonio Martinez-Sanchez, Wolfgang Baumeister, Günther Gerisch
In recent years new methodologies and workflow pipelines for acquiring correlated fluorescence microscopy and volume electron microscopy datasets have been extensively described and made accessible to users of different levels. Post-acquisition image processing, and particularly correlation of the optical and electron data in a single integrated three-dimensional framework can be key for extracting valuable information, especially when imaging large sample volumes such as whole cells or tissu... Read more
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
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
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
Acidic microenvironments created by bacterial clusters thriving in a polysaccharide matrix could be behind localized tooth decay. Jin Xiao of the University of Rochester Medical Center and Geelsu Hwang of the University of Pennsylvania with colleagues in the US mapped acidity changes across tooth enamel caused by the microstructure of dental plaque: a film of bacteria and the polysaccharide matrix they secrete. Using fluorescence microscopy, they studied the 3D architecture of plaque that for... Read more
Jin Xiao, Anderson T Hara, Dongyeop Kim, Domenick T Zero, Hyun Koo et al.
Neural circuitry in the lumbar spinal cord governs two principal features of locomotion, rhythm and pattern, which reflect intra- and interlimb movement. These features are functionally organized into a hierarchy that precisely controls stepping in a stereotypic, speed-dependent fashion. Here, we show that a specific component of the locomotor pattern can be independently manipulated…Read more
Amanda M. Pocratsky, Darlene A. Burke, Johnny R. Morehouse, Jason E. Beare, Amberly S. Riegler, Pantelis Tsoulfas, Gregory J. R. States, Scott R. Whittemore & David S. K. Magnuson
Lasers for Innovative Solutions, LLC (L4iS) is developing a new class of tomography technology with the aim of allowing material characterization in three dimensions with sub-micron resolution. The method uses a nanosecond, Q-switched, pulsed ultraviolet laser coupled with high-resolution imaging to generate highly detailed specimen models. Using this system, sequential images similar to light-sheet fluorescence microscopy are used to digitally reconstruct the specimen.Read more
Brian Reinhardt and Benjamin Hall, L4iS (USA)
Ali Ertürk and his collaborators described a novel histo-chemical technique to clear spinal cord tissue of adult mice for fluorescence microscopy imaging of the intact spinal cord.
Previously, the high lipid content of the spinal cord tissue in adult mice allowed imaging of the spinal cord only through destructive histological methods, making the tracing of complete axons impossible. As applied in this study, the improved histo-chemistry enabled Ertürk and his colleagues to show that... Read more
Ali Ertürk, Christoph P Mauch, Farida Hellal, Friedrich Förstner, Tara Keck, Klaus Becker, Nina Jährling, Heinz Steffens, Melanie Richter, Mark Hübener, Edgar Kramer, Frank Kirchhoff, Hans Ulrich Dodt & Frank Bradke