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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Structural Evolution of Highly Active Multicomponent Catalysts for Selective Propylene Oxidation

Structural Evolution of Highly Active Multicomponent Catalysts for Selective Propylene Oxidation

Multicomponent Bi-Mo-Fe-Co oxide catalysts prepared via flame spray pyrolysis were tested for selective propylene oxidation, showing high conversion (>70%) and selectivity (>85%) for acrolein and acrylic acid at temperatures of 330 ◦C. During extended time-on-stream tests (5–7 days), the catalysts retained high activity while undergoing diverse structural changes. This was evident on: (a) the atomic scale, using powder X-ray diffraction, Raman spectroscopy, X-ray absorption spectros... Read more

Paul Sprenger, Thomas L Sheppard, Jussi-Petteri Suuronen, Abhijeet Gaur, Federico Benzi and Jan-Dierk Grunwaldt

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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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Allometry and integration do not strongly constrain beak shape evolution in large-billed (Corvus macrorhynchos) and carrion crows (Corvus corone)

Allometry and integration do not strongly constrain beak shape evolution in large-billed (Corvus macrorhynchos) and carrion crows (Corvus corone)

Here, to evaluate the intensity of evolutionary constraints on avian beak shape more appropriately, we selected large billed (Corvus macrorhynchos) and carrion crows (Corvus corone) as study objects. These landbird species seem to experience selection pressures favoring a departure from an allometric trajectory. A landmark based geometric morphometric approach using three dimensional reconstructions of CT scan images revealed that only 45.4% of the total shape variation was explained by allom... Read more

Takeshi Yamasaki, Sou Aoki, Masayoshi Tokita

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In situ characterization of immiscible three-phase flow at the pore scale for a water-wet carbonate rock

In situ characterization of immiscible three-phase flow at the pore scale for a water-wet carbonate rock

X-ray micro-tomography is used to image the pore-scale configurations of fluid in a rock saturated with three phases – brine, oil and gas – mimicking a subsurface reservoir, at high pressure and temperature. We determine pore occupancy during a displacement sequence that involves waterflooding, gas injection and water re-injection. In the water-wet sample considered, brine occupied the smallest pores, gas the biggest, while oil occupied pores of intermediate size and is displaced ... Read more

Alessio Scanziani, Kamaljit Singh, Tom Bultreys, Branko Bijeljic, Martin J. Blunt

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Ultrastructural Characterization of Flashing Mitochondria

Ultrastructural Characterization of Flashing Mitochondria

Mitochondria undergo spontaneous transient elevations in matrix pH associated with drops in mitochondrial membrane potential. These mitopHlashes require a functional respiratory chain and the profusion protein optic atrophy 1, but their mechanistic basis is unclear. To gain insight on the origin of these dynamic events, we resolved the ultrastructure of flashing mitochondria by correlative light and electron microscopy. HeLa cells expressing the matrix-targeted pH probe mitoSypHer were screen... Read more

Manon Rosselin, Paula Nunes-Hasler, and Nicolas Demaurex

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High-resolution structures of HIV-1 Gag cleavage mutants determine structural switch for virus maturation

High-resolution structures of HIV-1 Gag cleavage mutants determine structural switch for virus maturation

HIV-1 maturation occurs via multiple proteolytic cleavages of the Gag polyprotein, causing rearrangement of the virus particle required for infectivity. (…) How individual cleavages contribute to changes in protein structure and interactions, and how the mature, conical capsid forms, are poorly understood. Here, we employed cryoelectron tomography to determine morphology and high-resolution CA lattice structures for HIV1 derivatives in which Gag cleavage sites are mutated. These analyse... Read more

Simone Mattei, Aaron Tan, Barbel Glass, Barbara Muller, Hans-Georg Krausslich, and John A. G. Briggs

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Partial dissolution of carbonate rock grains during reactive CO2-saturated brine injection under reservoir conditions

Partial dissolution of carbonate rock grains during reactive CO2-saturated brine injection under reservoir conditions

Our novel procedure of injecting oil after reactive transport has revealed previously unidentified (ghost) regions of partially-dissolved grains of carbonate rock. X-ray micro-tomography and FIB-SEM techniques were used to identify and resolve these ghost regions in three-dimensions at the nm- to µm-scale. Considering the solid part of the ghost regions as macro (bulk) pore space can result in the overestimation of porosity and permeability predi... Read more

Kamaljit Singh , Benaiah U. Anabaraonye , Martin J. Blunt , John Crawshaw

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Morphology of mitochondria in spatially restricted axons revealed by cryo-electron tomography

Morphology of mitochondria in spatially restricted axons revealed by cryo-electron tomography

Neurons project axons to local and distal sites and can display heterogeneous morphologies with limited physical dimensions that may influence the structure of large organelles such as mitochondria. Using cryo-electron tomography (cryo-ET), we characterized native environments within axons and presynaptic varicosities to examine whether spatial restrictions within these compartments influence the morphology of mitochondria. Segmented tomographic reconstructions revealed distinctive morphologi... Read more

Tara D. Fischer, Pramod K. Dash, Jun Liu, M. Neal Waxham

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Operative Anatomy of the Human Skull: A Virtual Reality Expedition

Operative Anatomy of the Human Skull: A Virtual Reality Expedition

The human cranial vault possesses an incredible, complex anatomical intricacy. Bridging the divide between 2-dimensional (2D) learning resources and the 3-dimensional (3D) world in which the anatomy becomes clinically relevant poses an intellectual challenge. Advances in computer graphics and modelling technologies have allowed increasingly accurate and representative resources to supplement cadaveric dissection specimens. To create accurate v... Read more

Benjamin K Hendricks, MD Akash J Patel, MD Jerome Hartman Mark F Seifert, PhD Aaron Cohen-Gadol, MD, MSc, MBA

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Metal-Organic Framework Crystal-Glass Composites

Metal-Organic Framework Crystal-Glass Composites

The majority of research into metal-organic frameworks (MOFs) focuses on their crystalline nature. However, in recent research the vitrification of a number of MOFs has been revealed. We propose that the solid-liquid phase transitions involved in MOF-glass formation can provide unique opportunities for the creation of a new class of functional, stable and porous composite materials. Described herein is the design, synthesis, and characterisation of novel metal-organic framework (MOF) crystal-... Read more

Jingwei Hou, Christopher W. Ashling, Sean M. Collins, Andraž Krajnc, Chao Zhou, Louis Longley, Duncan N. Johnstone, Philip A. Chater, Shichun Li, François-Xavier Coudert, David A. Keen, Paul A. Midgley, Gregor Mali, Vicki Chen, Thomas Bennett

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Digitizing extant bat diversity: An open-access repository of 3D μCT-scanned skulls for research and education

Digitizing extant bat diversity: An open-access repository of 3D μCT-scanned skulls for research and education

Biological specimens are primary records of organismal ecology and history. As such, museum collections are invaluable repositories for testing ecological and evolutionary hypotheses across the tree of life. Digitizing and broadly sharing the phenotypic data from these collections serves to expand the traditional reach of museums, enabling widespread data sharing, collaboration, and education at an unprecedented scale. In recent years, μCT-scanning has been adopted as one way for efficiently... Read more

Jeff J. Shi, Erin P. Westeen, Daniel L. Rabosky

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3D cephalometric analysis using Magnetic Resonance Imaging: validation of accuracy and reproducibility

3D cephalometric analysis using Magnetic Resonance Imaging: validation of accuracy and reproducibility

The aim of this study was to validate geometric accuracy and in vivo reproducibility of landmark-based cephalometric measurements using high-resolution 3D Magnetic Resonance Imaging (MRI) at 3 Tesla. (…) In conclusion, this study demonstrates that accurate and reproducible 3D cephalometric analysis can be performed without exposure to ionizing radiation using MRI.

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Alexander Juerchott, Muhammad Abdullah Saleem, Tim Hilgenfeld, Christian Freudlsperger, Sebastian Zingler, Christopher J. Lux, Martin Bendszus & Sabine Heiland

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Simulation Analysis on Water’s Micro Seepage Laws under Different Pressure Gradients Using Computed Tomography Method

Simulation Analysis on Water’s Micro Seepage Laws under Different Pressure Gradients Using Computed Tomography Method

The aim of this paper was to develop a model that can characterize the actual micropore structures in coal and gain an in-depth insight into water’s seepage rules in coal pores under different pressure gradients from a microscopic perspective. To achieve this goal, long-flame coals were first scanned by an X-ray 3D microscope; then, through a representative elementary volume (REV) analysis, the optimal side length was determined to be 60 μm; subsequently, by using Avizo software, the coal ... Read more

Gang Zhou, Lei Qiu, Wenzheng Zhang, and Jiao Xue

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Estimating the Effective Elastic Parameters of Nodular Cast Iron from Micro-Tomographic Imaging and Multiscale Finite Elements: Comparison between Numerical and Experimental Results

Estimating the Effective Elastic Parameters of Nodular Cast Iron from Micro-Tomographic Imaging and Multiscale Finite Elements: Comparison between Numerical and Experimental Results

We describe in detail a methodology to estimate the effective elastic parameters of nodular cast iron, using micro-tomography in conjunction with multiscale finite elements. We discuss the adjustment of the image acquisition parameters, address the issue of the representative-volume choice, and present a brief discussion on image segmentation. In addition, the finite-element computational implementation developed to estimate the effective elastic parameters from segmented microstructural imag... Read more

Andre Pereira, Marcio Costa, Carla Anflor, Juan Pardal and Ricardo Leiderman

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Tomographic investigation of the effects of second phases on the biodegradation and nano-mechanical performance of a Mg-Zn-Ca alloy

Tomographic investigation of the effects of second phases on the biodegradation and nano-mechanical performance of a Mg-Zn-Ca alloy

A combination of 3D tomography techniques provides direct evidence that links the phase assemblage to the bio-corrosion behaviour of a magnesium-zinc-calcium (Mg-Zn-Ca) alloy. The true shape, connectivity and volume fraction of the components have been determined using focused ion beam (FIB) tomography. The mechanism of the effect of the components with different morphologies on biodegradation was studied with the help of FIB. Micro X-ray CT (MicroCT) was used to investigate the degradation o... Read more

Y.Lu, R.G.Ding, Y.L.Chiu, I.P.Jones

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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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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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STIM1 promotes migration, phagosomal maturation and antigen cross-presentation in dendritic cells

STIM1 promotes migration, phagosomal maturation and antigen cross-presentation in dendritic cells

Antigen cross-presentation by dendritic cells (DC) stimulates cytotoxic T cell activation to promote immunity to intracellular pathogens, viruses and cancer. Phagocytosed antigens generate potent T cell responses, but the signalling and trafficking pathways regulating their cross-presentation are unclear. Here, we show that ablation of the store-operated-Ca2+-entry regulator STIM1 in mouse myeloid cells impairs cross-presentation and DC migration in vivo and in vitro. Stim1... Read more

Paula Nunes-Hasler, Sophia Maschalidi, Carla Lippens, Cyril Castelbou, Samuel Bouvet, Daniele Guido, Flavien Bermont, Esen Y. Bassoy, Nicolas Page, Doron Merkler, Stéphanie Hugues, Denis Martinvalet, Bénédicte Manoury & Nicolas Demaurex

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Effects of Porosity on Mechanical Properties and Corrosion Resistances of PM-Fabricated Porous Ti-10Mo Alloy

Effects of Porosity on Mechanical Properties and Corrosion Resistances of PM-Fabricated Porous Ti-10Mo Alloy

Porous binary Ti-10Mo alloys were prepared using non-spherical titanium, molybdenum powders by the powder metallurgy (PM) space holder technique. Based on the three-dimensional analysis of porosity characteristics, a detailed assessment of the effects of porosity on mechanical properties and corrosion resistances in phosphate-buffered saline (PBS) was carried out. For comparison, PM-fabricated CP-Ti with 50.5% porosity sintered at 1200 °C for 2 h and dense Ti-10Mo alloy sintered at 1450 °C ... Read more

Wei Xu, Xin Lu, Bing Zhang, Chengcheng Liu, Shaomin Lv, Shidi Yang and Xuanhui Qu

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High-resolution synchrotron-based X-ray microtomography as a tool to unveil the three-dimensional neuronal architecture of the brain

High-resolution synchrotron-based X-ray microtomography as a tool to unveil the three-dimensional neuronal architecture of the brain

The assessment of neuronal number, spatial organization and connectivity is fundamental for a complete understanding of brain function. However, the evaluation of the three-dimensional (3D) brain cytoarchitecture at cellular resolution persists as a great challenge in the field of neuroscience. In this context, X-ray microtomography has shown to be a valuable non-destructive tool for imaging a broad range of samples, from dense materials to soft biological specimens, arisen as a new method fo... Read more

Matheus de Castro Fonseca, Bruno Henrique Silva Araujo, Carlos Sato Baraldi Dias, Nathaly Lopes Archilha, Dionísio Pedro Amorim Neto, Esper Cavalheiro, Harry Westfahl Jr, Antônio José Roque da Silva, Kleber Gomes Franchini

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Over the rainbow? Micro-CT scanning to non-destructively study Roman and early medieval glass bead manufacture

Over the rainbow? Micro-CT scanning to non-destructively study Roman and early medieval glass bead manufacture

The usefulness of desktop Micro-CT scanners for the study of archaeological artefacts is demonstrated in a non-destructive study of manufacturing methods of Roman and Early Medieval monochrome and polychrome glass beads. Differences in glass colours show up in these scans as differences in attenuation. The presence and distribution of bubbles and various inclusions (metal, opacifier) are also well visible. Shaft shapes and patterns of bubbles inside the glass make it possible in most cases to... Read more

D.J.M.Ngan-Tillard, D.J.Huisman, F.Corbella, A.Van Nass

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