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.

Computational fluid dynamics with imaging of cleared tissue and of in vivo perfusion predicts drug uptake and treatment responses in tumours

Computational fluid dynamics with imaging of cleared tissue and of in vivo perfusion predicts drug uptake and treatment responses in tumours

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

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VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology

VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology

Despite advances in imaging, image-based vascular systems biology has remained challenging because blood vessel data are often available only from a single modality or at a given spatial scale, and cross-modality data are difficult to integrate.

Therefore, there is an exigent need for a multimodality pipeline that enables ex vivo vascular imaging with magnetic resonance imaging, computed tomography and optical microscopy of the same sample, while permitting imaging with complementary c... Read more

Akanksha Bhargava, Benjamin Monteagudo, Priyanka Kushwaha, Janaka Senarathna, Yunke Ren, Ryan C. Riddle , Manisha Aggarwal and Arvind P. Pathak

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Regional diversity in the murine cortical vascular network is revealed by synchrotron X-ray tomography and is amplified with age

Regional diversity in the murine cortical vascular network is revealed by synchrotron X-ray tomography and is amplified with age

Cortical bone is permeated by a system of pores, occupied by the blood supply and osteocytes. With ageing, bone mass reduction and disruption of the microstructure are associated with reduced vascular supply. Insight into the regulation of the blood supply to the bone could enhance the understanding of bone strength determinants and fracture healing. Using synchrotron radiation-based computed tomography, the distribution of vascular canals and osteocyte lacunae was assessed in murine cortica... Read more

J.A. Núñez; A. Goring; B. Javaheri; H. Razi; D. Gomez-Nicola; E. Hesse; A.A. Pitsillides; P.J. Thurner; P. Schneider; E. Clarkin

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Optical tissue clearing and machine learning can precisely characterize extravasation and blood vessel architecture in brain tumors

Optical tissue clearing and machine learning can precisely characterize extravasation and blood vessel architecture in brain tumors

Precise methods for quantifying drug accumulation in brain tissue are currently very limited, challenging the development of new therapeutics for brain disorders. Transcardial perfusion is instrumental for removing the intravascular fraction of an injected compound, thereby allowing for ex vivo assessment of extravasation into the brain. However, pathological remodeling of tissue microenvironment can affect the efficiency of transcardial perfusion, which has been largely overlooked.

We... Read more

Serhii Kostrikov, Kasper B. Johnsen, Thomas H. Braunstein, Johann M. Gudbergsson, Frederikke P. Fliedner, Elisabeth A. A. Obara, Petra Hamerlik, Anders E. Hansen, Andreas Kjaer, Casper Hempel & Thomas L. Andresen

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Optical Resolution Photoacoustic Microscopy of Ovary and Fallopian Tube

Optical Resolution Photoacoustic Microscopy of Ovary and Fallopian Tube

Ovarian cancer is the leading cause of death among gynecological cancers, but is poorly amenable to preoperative diagnosis. In this study, we investigate the feasibility of “optical biopsy,” using high-optical-resolution photoacoustic microscopy (OR-PAM) to quantify the microvasculature of ovarian and fallopian tube tissue. The technique is demonstrated using excised human ovary and fallopian tube specimens imaged immediately after surgery.
This report describes the first applicatio... Read more

Bin Rao, Xiandong Leng, Yifeng Zeng, Yixiao Lin, Ruimin Chen, Qifa Zhou, Andrea R. Hagemann, Lindsay M. Kuroki, Carolyn K. McCourt, David G. Mutch, Matthew A. Powell, Ian S. Hagemann & Quing Zhu

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Regional Aneurysm Wall Enhancement is Affected by Local Hemodynamics: A 7T MRI Study

Regional Aneurysm Wall Enhancement is Affected by Local Hemodynamics: A 7T MRI Study

Aneurysm wall enhancement has been proposed as a biomarker for inflammation and instability. However, the mechanisms of aneurysm wall enhancement remain unclear. We used 7T MR imaging to determine the effect of flow in different regions of the wall.

Twenty-three intracranial aneurysms imaged with 7T MR imaging and 3D angiography were studied with computational fluid dynamics. Local flow conditions were compared between aneurysm wall enhancement and nonenhanced regions. Aneurysm wall en... Read more

S. Hadad, F. Mut, B.J. Chung, J.A. Roa, A.M. Robertson, D.M. Hasan, E.A. Samaniego and J.R. Cebral

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Quantified growth of the human embryonic heart

Quantified growth of the human embryonic heart

The size and growth patterns of the components of the human embryonic heart have remained largely undefined.

To provide these data, three-dimensional heart models were generated from immunohistochemically stained sections of ten human embryonic hearts ranging from Carnegie stage 10 to 23. Fifty-eight key structures were annotated and volumetrically assessed. Sizes of the septal foramina and atrioventricular canal opening were also measured. The heart grows exponentially throughout embr... Read more

Jaeike W. Faber, Jaco Hagoort, Antoon F. M. Moorman, Vincent M. Christoffels, Bjarke Jensen

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High-resolution mapping of brain vasculature and its impairment in the hippocampus of Alzheimer’s disease mice

High-resolution mapping of brain vasculature and its impairment in the hippocampus of Alzheimer’s disease mice

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

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Precise Cerebral Vascular Atlas in Stereotaxic Coordinates of Whole Mouse Brain

Precise Cerebral Vascular Atlas in Stereotaxic Coordinates of Whole Mouse Brain

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

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Ultrasound Molecular Imaging of Renal Cell Carcinoma: VEGFR targeted therapy monitored with VEGFR1 and FSHR targeted microbubbles

Ultrasound Molecular Imaging of Renal Cell Carcinoma: VEGFR targeted therapy monitored with VEGFR1 and FSHR targeted microbubbles

Recent treatment developments for metastatic renal cell carcinoma offer combinations of immunotherapies or immunotherapy associated with tyrosine kinase inhibitors (TKI). There is currently no argument to choose one solution or another. Easy-to-use markers to assess longitudinal responses to TKI are necessary to determine when to switch to immunotherapies. These new markers will enable an earlier adaptation of therapeutic strategy in order to prevent tumor development, unnecessary toxicity an... Read more

Alexandre Ingels, Ingrid Leguerney, Paul-Henry Cournède, Jacques Irani, Sophie Ferlicot, Catherine Sébrié, Baya Benatsou, Laurène Jourdain, Stephanie Pitre-Champagnat, Jean-Jacques Patard & Nathalie Lassau

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Multi-Scale Digital Image Correlation Analysis of In Situ Deformation of Open-Cell Porous Ultra-High Molecular Weight Polyethylene Foam

Multi-Scale Digital Image Correlation Analysis of In Situ Deformation of Open-Cell Porous Ultra-High Molecular Weight Polyethylene Foam

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

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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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Vascular structure of the earliest shark teeth

Vascular structure of the earliest shark teeth

Here we use synchrotron tomography to characterise dental vasculature in the oldest known tooth-bearing sharks, Leonodus carlsi Mader, 1986 and Celtiberina maderi Wang, 1993. Three dimensional reconstruction of the vascular system and microstructure of both taxa revealed a complex and dense network of canals, including horizontal, ascending and secondary bifurcated canals, as well as histological features consistent with an osteodont histotype. However, L. carlsi and C. maderi also exhibit si... Read more

Carlos Martinez-Perez, Alba Martin-Lazaro, Humberto G Ferron, Martina Kirstein, Philip C.J. Donoghue, Hector Botella

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Spatiotemporal endothelial cell – pericyte association in tumors as shown by high resolution 4D intravital imaging

Spatiotemporal endothelial cell – pericyte association in tumors as shown by high resolution 4D intravital imaging

Endothelial cells and pericytes are integral cellular components of the vasculature with distinct interactive functionalities. To study dynamic interactions between these two cells we created two transgenic animal lines. A truncated eNOS (endothelial nitric oxide synthase) construct was used as a GFP tag for endothelial cell evaluation and an inducible Cre-lox recombination, under control of the Pdgfrb (platelet derived growth factor receptor beta) promoter, was created for pericyte assessmen... Read more

Ann L. B. Seynhaeve, Douwe Oostinga, Rien van Haperen, Hanna M. Eilken, Susanne Adams, Ralf H. Adams & Timo L. M. ten Hagen

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Human liver segments: role of cryptic liver lobes and vascular physiology in the development of liver veins and left-right asymmetry

Human liver segments: role of cryptic liver lobes and vascular physiology in the development of liver veins and left-right asymmetry

Couinaud based his well-known subdivision of the liver into (surgical) segments on the branching order of portal veins and the location of hepatic veins. However, both segment boundaries and number remain controversial due to an incomplete understanding of the role of liver lobes and vascular physiology on hepatic venous development. Human embryonic livers (5–10 weeks of development) were visualized with Amira 3D-reconstruction and Cinema 4D-remodeling software.

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Jill P. J. M. Hikspoors, Mathijs M. J. P. Peeters, Nutmethee Kruepunga, Hayelom K. Mekonen, Greet M. C. Mommen, S. Eleonore Köhler & Wouter H. Lamers

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University of Glasgow uses Amira software to analyze vascular structures

University of Glasgow uses Amira software to analyze vascular structures

The vascular (arterial or venous) wall is a fascinating structure. At the simplest level, we can think of the wall as being composed of three distinct, but interacting, layers . The vascular wall changes its structure in conditions such as hypertension which can cause a thickening of the wall. Unfortunately, the details of this ‘remodeling’ process are poorly understood.

Therefore, studying the 3D architecture may provide vital clues for future therapeutic targets.

R... Read more

Dr. Craig J Daly, School of Life Sciences, College of Medical Veterinary & Life Sciences, University of Glasgow

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