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.

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RF-induced heating in tissue near bilateral DBS implants during MRI at 1.5 T and 3T: The role of surgical lead management

RF-induced heating in tissue near bilateral DBS implants during MRI at 1.5 T and 3T: The role of surgical lead management

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

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Hyperpolarized 13C MR metabolic imaging can detect neuroinflammation in vivo in a multiple sclerosis murine model

Hyperpolarized 13C MR metabolic imaging can detect neuroinflammation in vivo in a multiple sclerosis murine model

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) Read more

Caroline Guglielmetti, Chloé Najac, Alessandro Didonna, Annemie Van der Linden, Sabrina M. Ronen, and Myriam M. Chaumeil

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Insights into data with the KAUST Visualization Core Lab

Insights into data with the KAUST Visualization Core Lab

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

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Using micro-computed tomography to reveal the anatomy of adult Diaphorina citri Kuwayama (Insecta: Hemiptera, Liviidae) and how it pierces and feeds within a citrus leaf

Using micro-computed tomography to reveal the anatomy of adult Diaphorina citri Kuwayama (Insecta: Hemiptera, Liviidae) and how it pierces and feeds within a citrus leaf

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

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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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3D electron tomography of brain tissue unveils distinct Golgi structures that sequester cytoplasmic contents in neurons

3D electron tomography of brain tissue unveils distinct Golgi structures that sequester cytoplasmic contents in neurons

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…

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Maria Rosario Fernandez-Fernandez, Desire Ruiz-Garcia, Eva Martin-Solana, Francisco Javier Chichon, Jose L. Carrascosa, Jose-Jesus Fernandez

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Patient-specific anatomical model for deep brain stimulation based on 7 Tesla MRI

Patient-specific anatomical model for deep brain stimulation based on 7 Tesla MRI

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

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A detailed canine brain label map for neuroimaging analysis

A detailed canine brain label map for neuroimaging analysis

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

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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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Distribution of Serotonin-Immunoreactive Neurons in the Brain and Gnathal Ganglion of Caterpillar Helicoverpa armigera

Distribution of Serotonin-Immunoreactive Neurons in the Brain and Gnathal Ganglion of Caterpillar Helicoverpa armigera

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

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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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An adult brain atlas reveals broad neuroanatomical changes in independently evolved populations of Mexican cavefish

An adult brain atlas reveals broad neuroanatomical changes in independently evolved populations of Mexican cavefish

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

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Mitochondria-rough-ER contacts in the liver regulate systemic lipid homeostasis

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

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Neuroanatomical tract-tracing techniques that did go viral

Neuroanatomical tract-tracing techniques that did go viral

Neuroanatomical tracing methods remain fundamental for elucidating the complexity of brain circuits. During the past decades, the technical arsenal at our disposal has been greatly enriched, with a steady supply of fresh arrivals. This paper provides a landscape view of classical and modern tools for tract-tracing purposes. Focus is placed on methods that have gone viral, i.e., became most widespread used and fully reliable.

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Jose L. Lanciego; Floris G. Wouterlood

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Cognition based bTBI mechanistic criteria; a tool for preventive and therapeutic innovations

Cognition based bTBI mechanistic criteria; a tool for preventive and therapeutic innovations

Blast-induced traumatic brain injury has been associated with neurodegenerative and neuropsychiatric disorders. To date, although damage due to oxidative stress appears to be important, the specific mechanistic causes of such disorders remain elusive. Here, to determine the mechanical variables governing the tissue damage eventually cascading into cognitive deficits, we performed a study on the mechanics of rat brain under blast conditions. To this end, experiments were carried out to analyse... Read more

Daniel Garcia-Gonzalez, Nicholas S. Race, Natalie L. Voets, Damian R. Jenkins, Stamatios N. Sotiropoulos, Glen Acosta, Marcela Cruz-Haces, Jonathan Tang, Riyi Shi & Antoine Jérusalem

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Differentiation and Characterization of Excitatory and Inhibitory Synapses by Cryo-electron Tomography and Correlative Microscopy

Differentiation and Characterization of Excitatory and Inhibitory Synapses by Cryo-electron Tomography and Correlative Microscopy

As key functional units in neural circuits, different types of neuronal synapses play distinct roles in brain information processing, learning, and memory. Synaptic abnormalities are believed to underlie various neurological and psychiatric disorders. Here, by combining cryo-electron tomography and cryo-correlative light and electron microscopy, we distinguished intact excitatory and inhibitory synapses of cultured hippocampal neurons, and visualized the in situ 3D organization of ... Read more

Chang-Lu Tao, Yun-Tao Liu, Rong Sun, Bin Zhang, Lei Qi, Sakar Shivakoti, Chong-Li Tian, Peijun Zhang, Pak-Ming Lau, Z. Hong Zhou and Guo-Qiang Bi

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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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3D visualization and deep-learning reveal complex parasite networks in behaviorally manipulated ants

3D visualization and deep-learning reveal complex parasite networks in behaviorally manipulated ants

Microbial parasites may behave collectively to manipulate their host’s behavior. We examine adaptations of a microbial parasite in its natural environment: the body of its coevolved and manipulated host.

Electron microscopy and 3D reconstructions of host and parasite tissues reveal that this fungus invades muscle fibers throughout the ant’s body but leaves the brain intact, and that the fungal cells connect to form extensive networks.

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Maridel A. Fredericksena, Yizhe Zhangb, Missy L. Hazenc, Raquel G. Loretoa,d, Colleen A. Mangoldd,e, Danny Z. Chenb, and David P. Hughes, Department of Entomology, Pennsylvania State University

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High-resolution ultramicroscopy of the developing and adult nervous system in optically cleared Drosophila melanogaster

High-resolution ultramicroscopy of the developing and adult nervous system in optically cleared Drosophila melanogaster

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

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Full reconstruction of large lobula plate tangential cells in Drosophila from a 3D EM dataset

Full reconstruction of large lobula plate tangential cells in Drosophila from a 3D EM dataset

With the advent of neurogenetic methods, the neural basis of behavior is presently being analyzed in more and more detail. This is particularly true for visually driven behavior of Drosophila melanogaster where cell-specific driver lines exist that, depending on the combination with appropriate effector genes, allow for targeted recording, silencing and optogenetic stimulation of individual cell-types. Together with detailed connectomic data of large parts of the fly optic lobe, this has rece... Read more

Kevin M. Boergens , Christoph Kapfer, Moritz Helmstaedter, Winfried Denk, Alexander Borst

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