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.
Deep brain stimulation (DBS) requires accurate localization of the anatomical target structure, and the precise placement of the DBS electrode within it. Ultra-high field 7 Tesla (T) MR images can be utilized to create patient-specific anatomical 3D models of the subthalamic nuclei (STN) to enhance pre-surgical DBS targeting as well as post-surgical visualization of the DBS lead position and orientation. We validated the accuracy of the 7T imaging-based patient-specific model of the STN and m... Read more
Yuval Duchin, Reuben R. Shamir, Remi Patriat, Jinyoung Kim, Jerrold L. Vitek, Guillermo Sapiro, Noam Harel
Accumulating evidence indicates the critical importance of cerebrovascular dysfunction in the pathogenesis of Alzheimer’s disease (AD). However, systematic comparative studies on the precise brain vasculature of wild-type and AD model mice are still rare. Using an image optimization method for analyzing Micro-Optical Sectioning Tomography (MOST) data, we generated cross-scale whole-brain 3D atlases that cover the entire vascular system from large vessels down to smallest capillaries at ... Read more
Xiaochuan Zhang, Xianzhen Yin, Jingjing Zhang, Anan Li, Hui Gong, Qingming Luo, Haiyan Zhang, Zhaobing Gao, Hualiang Jiang
Understanding amazingly complex brain functions and pathologies requires a complete cerebral vascular atlas in stereotaxic coordinates. Making a precise atlas for cerebral arteries and veins has been a century-old objective in neuroscience and neuropathology. Using micro-optical sectioning tomography (MOST) with a modified Nissl staining method, we acquired five mouse brain data sets containing arteries, veins, and microvessels. Based on the brain-wide vascular spatial structures and brain re... Read more
Benyi Xiong, Anan Li, Yang Lou, Shangbin Chen, Ben Long, Jie Peng, Zhongqin Yang, Tonghui Xu, Xiaoquan Yang, Xiangning Li, Tao Jiang, Qingming Luo and Hui Gong
The purpose of the study is the development and evaluation of the informativeness of the author’s 3D nephrometric score application to predict the probability of intraoperative and postoperative complications in kidney operations.
The study includes 264 patients who underwent surgical treatment of renal tumors, before that CT and 3D modeling were carried out. All patients underwent an analysis of the surgical intervention complexity on the C-index, PADUA, R.E.N.A.L., and developed 3D... Read more
Georgiy Andreevich Mashin, Vasiliy Vladimirovich Kozlov, Denis Vladimirovich Chinenov, Yaroslav Nikolaevich Chernov, Alexandra Vladimirovna Proskura, Dmitry Olegovich Korolev , Dmitry Georgievich Tsarichenko, Leonid Mikhailovich Rapoport and Evgeniy Valerievich Shpot
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
Understanding the uptake of a drug by diseased tissue, and the drug’s subsequent spatiotemporal distribution, are central factors in the development of effective targeted therapies. However, the interaction between the pathophysiology of diseased tissue and individual therapeutic agents can be complex, and can vary across tissue types and across subjects. Here, we show that the combination of mathematical modelling, high-resolution optical imaging of intact and optically cleared tumour tiss... Read more
Angela d’Esposito, Paul W. Sweeney, Morium Ali, Magdy Saleh, Rajiv Ramasawmy, Thomas A. Roberts, Giulia Agliardi, Adrien Desjardins, Mark F. Lythgoe, R. Barbara Pedley, Rebecca Shipley and Simon Walker-Samuel
Since its invention and commercialization in the 1950s, ultra-high molecular weight polyethylene (UHMWPE) has been known as a high-performance polymer successfully applied in diverse engineering systems ranging from strong ropes for naval demands and wear-resistant liners in bearings, transportation belts and heavy trucks in mines and quarries, through the lining of chemical vessels and disposable bags in bioreactors, to sophisticated products such as orthopaedic implants and replacements of ... Read more
Eugene S. Statnik, Codrutza Dragu, Cyril Besnard, Alexander J.G. Lunt, Alexey I. Salimon, Aleksey Maksimkin and Alexander M. Korsunsky
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
We demonstrate feasibility of the workflow by combining in vivo 2-photon microscopy and focused ion beam scanning electron microscopy (FIB/SEM) to dissect the role of astrocytic coverage in the persistence of dendritic spines.
Emerging 3D correlative light and electron microscopy (CLEM) approaches enable studying neuronal structure-function relations at unprecedented depth and precision. However, established protocols for the correlation of light and electron micrographs rely ... Read more
Manja Luckner,Steffen Burgold, Severin Filser, Maximilian Scheungrab, Yilmaz Niyaz, Eric Hummel, Gerhard Wanner, Jochen Herms