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.
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
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
Neuromuscular junction degeneration is a prominent aspect of sarcopenia, the age-associated loss of skeletal muscle integrity. Previously, we showed that muscle stem cells activate and contribute to mouse neuromuscular junction regeneration in response to denervation (Liu et al., 2015). Here, we examined gene expression profiles and neuromuscular junction integrity in aged mouse muscles, and unexpectedly found limited denervation despite a high level of degenerated neuromuscular junctions. In... Read more
Wenxuan Liu, Alanna Klose, Sophie Forman, Nicole D Paris, Lan Wei-LaPierre, Mariela Cortés-Lopéz, Aidi Tan, Morgan Flaherty, Pedro Miura, Robert T Dirksen, Joe V Chakkalakal
Microscopic organisms that penetrate calcareous structures by actively dissolving the carbonate matrix, namely microendoliths, have an important influence on the breakdown of marine carbonates.
Microscopic organisms that penetrate calcareous structures by actively dissolving the carbonate matrix, namely microendoliths, have an important influence on the breakdown of marine carbonates. The study of these microorganisms and the bioerosion traces they produce is crucial for understanding ... Read more
Philipp-Konrad Schätzle, Max Wisshak, Andreas Bick, André Freiwald, Alexander Kieneke
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
Access to MRI is limited for patients with DBS implants due to safety hazards, including radiofrequency heating of tissue surrounding the leads. Computational models provide an exquisite tool to explore the multi-variate problem of RF implant heating. We used a computational approach to assess RF heating around tips of bilateral DBS leads during MRI at 1.5T and 3T using realistic DBS lead models. A substantial difference was found between the SAR and temperature rise at the tip of right and l... Read more
Laleh Golestanirad, John Kirsch, Giorgio Bonmassar, Sean Downs, Behzad Elahi, Alastair Martin, Maria-Ida Iacono, Leonardo M. Angelone, Boris Keil, Lawrence L. Wald, Julie Pilitsis
Proinflammatory mononuclear phagocytes (MPs) play a crucial role in the progression of multiple sclerosis (MS) and other neurodegenerative diseases. Despite advances in neuroimaging, there are currently limited available methods enabling noninvasive detection of MPs in vivo. Interestingly, upon activation and subsequent differentiation toward a proinflammatory phenotype MPs undergo metabolic reprogramming that results in increased glycolysis and production of lactate. Hyperpolarized (HP)
Caroline Guglielmetti, Chloé Najac, Alessandro Didonna, Annemie Van der Linden, Sabrina M. Ronen, and Myriam M. Chaumeil
Through collaboration, the KAUST Visualization Core Lab (KVL) team augments the efforts and domain expertise of KAUST researchers by providing complimentary technical knowledge with exploratory visualization and analytic tools.
KVL’s multi-year collaboration with KAUST Distinguished Professor P. Magistretti and research scientist C. Calì’s KAUST-EPFL Alliance for Integrative Modelling of Brain Energy Metabolism project—itself a collaboration with the Swiss Blue Br... Read more
By the KAUST Visualization Core Lab team and Caitlin Clark
The Asian citrus psyllid (ACP), Diaphorina citri, is a harmful pest of citrus trees that transmits Candidatus Liberibacter spp. which causes Huanglongbing (HLB) (citrus greening disease); this is considered to be the most serious bacterial disease of citrus plants.
Here we detail an anatomical study of the external and internal anatomy (excluding the reproductive system) using micro-computed tomography (micro-CT). This is the first complete 3D micro-CT reconstruction o... Read more
Javier Alba-Tercedor, Wayne B. Hunter & Ignacio Alba-Alejandre
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
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
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…Read more
Maria Rosario Fernandez-Fernandez, Desire Ruiz-Garcia, Eva Martin-Solana, Francisco Javier Chichon, Jose L. Carrascosa, Jose-Jesus Fernandez
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
Dogs have recently become an important model species for comparative social and cognitive neuroscience. Brain template-related label maps are essential for functional magnetic resonance imaging (fMRI) data analysis, to localize neural responses. In this study, we present a detailed, individual-based, T1-weighted MRI-based brain label map used in dog neuroimaging analysis. Methods: A typical, medium-headed dog (a 7.5-year-old
male Golden Retriever) was selected from a cohort of ... Read more
Czeibert Kálmán, Andics Attila, Petneházy Örs, Kubinyi Enikő, Kálmán Czeibert
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
Serotonin (5-hydroxytryptamine, 5-HT) is an important biogenic amine that acts as a neural circuit modulator. It is widespread in the central nervous system of insects. However, little is known about the distribution of serotonin in the nervous system of the cotton bollworm Helicoverpa armigera. In the present study, we performed immunohistochemical experiments with anti-serotonin serum to examine the distribution of serotonin in the central nervous system of H. armigera larv... Read more
Qing-Bo Tang, Wei-Wei Song, Ya-Jun Chang, Gui-Ying Xie, Wen-Bo Chen* and Xin-Cheng Zhao
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
A shift in environmental conditions impacts the evolution of complex developmental and behavioral traits. The Mexican cavefish, Astyanax mexicanus, is a powerful model for examining the evolution of development, physiology, and behavior because multiple cavefish populations can be compared to an extant and ancestral-like surface population of the same species. Many behaviors have diverged in cave populations of A. mexicanus, and previous studies have shown that cavefish ha... Read more
Cody Loomis, View ORCID ProfileRobert Peuß, James Jaggard, Yongfu Wang, Sean McKinney, Stephen Raftopoulos, Austin Raftopoulos, Daniel Whu, Matthew Green, Suzanne E. McGaugh, Nicolas Rohner, Alex C. Keene, Erik R. Duboue
The clinical use of bioactive molecules in bone regeneration has been known to have side effects, which result from uncontrolled and supraphysiological doses.
In this study, we demonstrated the synergistic effect of two bioactive molecules, bone morphogenic protein-2 (BMP-2) and alendronate (ALN), by releasing them in a sequential manner. Collagen-hydroxyapatite composite scaffolds functionalized using BMP-2 are loaded with biodegradable microspheres where ALN is encapsulated.
Th... Read more
Dongtak Lee, Maierdanjiang Wufuer, Insu Kim, Tae Hyun Choi , Byung Jun Kim , Hyo Gi Jung, Byoungjun Jeon, Gyudo Lee, Ok Hee Jeon, Hak Chang & Dae Sung Yoon
To evaluate the ability of radiomic feature extraction and a machine learning algorithm to diferentiate between benign
and malignant indeterminate adrenal lesions on contrast-enhanced computed tomography (CT) studies.
Adrenal “incidentalomas” are adrenal lesions that are accidentally discovered during workup not related to the adrenal glands; they have an incidence as high as 5%. Small adrenal incidentalomas (<4 cm) with high attenuation values on pre-contrast CT(>10 H... Read more
Ahmed W. Moawad, Ayahallah Ahmed, David T. Fuentes, John D. Hazle, Mouhammed A. Habra, Khaled M. Elsayes
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