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.
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.
3D computational anatomy of the scaphoid and its waist for use in fracture treatment
A detailed understanding of scaphoid anatomy helps anatomic fracture reduction and optimal screw position. Therefore, we analyzed the size and shape variations of the cartilage and osseous surface, the distribution of volumetric bone mineral density (vBMD), and if the vBMD values differ between a peripheral and a central screw pathway?
Forty-three fresh frozen hand specimens (17 females, 26 males) were analysed with high-resolution peripheral quantitative computed tomography (HR-pQCT) ... Read more
Marc-Daniel Ahrend, Teun Teunis, Hansrudi Noser, Florian Schmidutz, Geoff Richards, Boyko Gueorguiev & Lukas Kamer
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
Decommissioning of the damaged Chernobyl nuclear reactor Unit 4 is a top priority for the global community. Before such operations begin, it is crucial to understand the behaviour of the hazardous materials formed during the accident. Since those materials formed under extreme and mostly unquantified conditions, modelling alone is insufficient to accurately predict their physical, chemical and, predominantly, mechanical behaviour. Meanwhile, knowledge of the mechanical characteristics of thos... Read more
C.Paraskevoulakos, J.P.Forna-Kreutzer, K.R.Hallam, C.P.Jones, T.B.Scott, C.Gausse, D.J.Bailey, C.A.Simpson, D.Liu, C.Reinhard, C.L.Corkhill, M.Mostafavi
Quantifying Microstructural Evolution in Moving Magma
Many of the grand challenges in volcanic and magmatic research are focused on understanding the dynamics of highly heterogeneous systems and the critical conditions that enable magmas to move or eruptions to initiate. However, we are usually unable to observe the processes directly. Here we give a short synopsis of the new capabilities and highlight the potential insights that in situ observation can provide. We present the first 3D data showing the evolving textural heterogeneity within a sh... Read more
Katherine J. Dobson1, Anja Allabar, Eloise Bretagne, Jason Coumans, Mike Cassidy, Corrado Cimarelli, Rebecca Coats, Thomas Connolley, Loic Courtois, Donald B. Dingwell, Danilo Di Genova, Benjamin Fernando, Julie L. Fife, Frey Fyfe, Stephan Gehne, Thomas Jones, Jackie E. Kendrick, Helen Kinvig, Stephan Kolzenburg, Yan Lavallée, Emma Liu, Edward W. Llewellin, Amber Madden-Nadeau, Kamel Madi, Federica Marone, Cerith Morgan, Julie Oppenheimer, Anna Ploszajski, Gavin Reid, Jenny Schauroth, Christian M. Schlepütz, Catriona Sellick, Jérémie Vasseur, Felix W. von Aulock, Fabian B. Wadsworth, Sebastian Wiesmaier and Kaz Wanelik
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