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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Micron-scale crack propagation in laser-irradiated enamel and dentine studied with nano-CT

Micron-scale crack propagation in laser-irradiated enamel and dentine studied with nano-CT

The aim of this study was to see the effect of Er:YAG laser irradiation in dentine and compare this with its effect in enamel. The mechanism of crack propagation in dentine was emphasised and its clinical implications were discussed. A possible mechanism is that laser radiation is transmitted down the dentinal tubules causing micro-cracks to form in the dentinal tubule walls that tend to be limited to this region. Crack might be a source of fracture as it represents a weak point and subsequen... Read more

Abtesam Aljdaimi, Hugh Devlin, Mark Dickinson, Timothy Burnett, Thomas J. A. Slater

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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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Three-dimensional Image Based Modelling of Transport Parameters in LithiumSulfur Batteries

Three-dimensional Image Based Modelling of Transport Parameters in LithiumSulfur Batteries

An elemental sulfur electrode was imaged with X-ray micro and nano computed tomography and segmented into its constituent phases. Morphological parameters including phase fractions, pore and particle size distributions were calculated directly from labelled image data, and flux based simulations were performed to determine the effective molecular diffusivity of the pore phase and electrical conductivity of the conductive carbon and binder phase, Deff and σeff, that can be used as an input fo... Read more

Chun Tan, Matthew D. R. Kok, Sohrab R. Daemi, Dan Brett and Paul Shearing

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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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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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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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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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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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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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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 method for deducing neck mobility in plesiosaurs, using the exceptionally preserved Nichollssaura borealis

A method for deducing neck mobility in plesiosaurs, using the exceptionally preserved Nichollssaura borealis

The elongate-necked aquatic plesiosaurs existed for 135 Myr during the Mesozoic. The function of this elongate neck is a point of debate. Using computed tomography and three-dimensional (3D) modelling, the range of motion (ROM) of the plesiosaur Nichollssaura borealis neck was assessed. To quantify the ROM, the intervertebral mobility was measured along the cervical vertebral column. This was done by manipulating the 3D models in the lateral and dorsoventral directions during two tri... Read more

Ramon S. Nagesan, Donald M. Henderson, Jason S. Anderson

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Ptychographic X-ray CT characterization of the osteocyte lacuno-canalicular network in a male rat's glucocorticoid induced osteoporosis model

Ptychographic X-ray CT characterization of the osteocyte lacuno-canalicular network in a male rat's glucocorticoid induced osteoporosis model

Ptychographic X-ray computed tomography (PXCT) is a quantitative imaging modality that non-destructively maps the 3D electron density inside an object with tens of nanometers spatial resolution. This method provides unique access to the morphology and structure of the osteocyte lacuno-canalicular network (LCN) and nanoscale density of the tissue in the vicinity of an osteocyte lacuna.  Our findings indicate that PXCT can non-destructively provide detailed, nanoscale information on the 3D org... Read more

Antonia Ciani, Hechmi Toumi, Stéphane Pallu, Esther H.R.Tsai, Ana Diaz, Manuel Guizar-Sicairos, Mirko Holler, Eric Lespessailles, Cameron M.Kewish | Synchrotron Soleil, France

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Functionally Sorted Laminated Material for Damage Resistance and Damage Tolerance

Functionally Sorted Laminated Material for Damage Resistance and Damage Tolerance

In this thesis, the damage mechanisms and failure behaviours of hybrid laminates panels due to out-of-plane impact and near-edge and on-edge impact were investigated. The impact tests include low-velocity dynamic impact test and quadra-static indentation. Compression after impact was conducted to discover the residual stiffness in the post-test samples and the improvement of damage resistance and damage tolerance are analysed. A novel testing and inspection method had been developed by combin... Read more

Shi Hua

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Visualizing the Carbon Binder Phase of Battery Electrodes in Three Dimensions

Visualizing the Carbon Binder Phase of Battery Electrodes in Three Dimensions

This study presents a technique to directly characterize the carbon and binder domain (CBD) in lithium-ion (Li-ion) battery electrodes in three dimensions and use it to determine the effective transport properties of a LiNi0.33Mn0.33Co0.33O2 (NMC) electrode. X-ray nanocomputed tomography (nano-CT) is used to image an electrode composed solely of carbon and binder, whereas focused ion beam–scanning electron microscopy is used to analyze cross-sect... Read more

Sohrab R. Daemi, Chun Tan, Tobias Volkenandt, Samuel J. Cooper, Anna Palacios-Padros, James Cookson, Dan J. L. Brett, and Paul R. Shearing

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Three-Dimensional In Situ XCT Characterisation and FE Modelling of Cracking in Concrete

Three-Dimensional In Situ XCT Characterisation and FE Modelling of Cracking in Concrete

An improved understanding of 3D cracking in concrete can be achieved by multiscale experiments and numerical modelling based on realistic microstructures, for the development of materials with higher strength, durability, and fracture resistance.

Three-dimensional (3D) characterisation and modelling of cracking in concrete have been always of great importance and interest in civil engineering. In this study, an in situ microscale X-ray computed tomography (XCT) test was carried out to ... Read more

Wenyuan Ren, Zhenjun Yang, Rajneesh Sharma, Samuel A. McDonald, Paul M. Mummery

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Secure corridor for infraacetabular screws in acetabular fracture fixation—a 3-D radiomorphometric analysis of 124 pelvic CT datasets

Secure corridor for infraacetabular screws in acetabular fracture fixation—a 3-D radiomorphometric analysis of 124 pelvic CT datasets

Acetabular fracture surgery is directed toward anatomical reduction and stable fixation to allow for the early functional rehabilitation of an injured hip joint. Recent biomechanical investigations have shown the superiority of using an additional screw in the infraacetabular (IA) region, thereby transfixing the separated columns to strengthen the construct by closing the periacetabular fixation frame. However, the inter-individual existence and variance concerning secure IA screw corridors a... Read more

Stephan Arlt, Hansrudi Noser, Andreas Wienke, Florian Radetzki, Gunther Olaf Hofmann, Thomas Mendel

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