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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Investigation of pressure drop in 3D replicated open-cell foams: Coupling CFD with experimental data on additively manufactured foams

Investigation of pressure drop in 3D replicated open-cell foams: Coupling CFD with experimental data on additively manufactured foams

Open-cell foams as structured catalyst supports are promising candidates for the design of high throughput catalytic processes. In this contribution, we employ a coupled numerical and experimental approach to assess the pressure losses in foams. (…) we explore virtually-generated foam models and their 3D printed replicas for a combined CFD and experimental study of fluid dynamics in foams. In particular, we focus our analysis on the low Reynolds number regime, where deviations between t... Read more

Mauro Bracconi, Matteo Ambrosetti, Obinna Okafor, Victor Sans, Xun Zhang, Xiaoxia Ou, Claudio Pereira Da Fonte, Xiaolei Fan, Matteo Maestri, Gianpiero Groppi, Enrico Tronconi

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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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Branching morphogenesis of the urinary collecting system in the human embryonic metanephros

Branching morphogenesis of the urinary collecting system in the human embryonic metanephros

An elaborate system of ducts collects urine from all nephrons, and this structure is known as the urinary collecting system (UCS). This study focused on how the UCS is formed during human embryogenesis. Fifty human embryos between the Carnegie stage (CS) 14 and CS23 were selected from the Kyoto Collection at the Congenital Anomaly Research Center of Kyoto University, Japan. Metanephroses, including the UCS, were segmented on serial digital virtual histological sections. Three-dimensional imag... Read more

Hana Ishiyama, Aoi Ishikawa, Haruka Kitazawa, Sena Fujii, Jun Matsubayashi, Shigehito Yamada, Tetsuya Takakuwa

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Nonuniformity in ligaments is a structural strategy for optimizing functionality

Nonuniformity in ligaments is a structural strategy for optimizing functionality

Ligaments serve as compliant connectors between hard tissues. In that role, they function under various load regimes and directions. The 3D structure of ligaments is considered to form as a uniform entity that changes due to function. The periodontal ligament (PDL) connects the tooth to the bone and sustains different types of loads in various directions. Using the PDL as a model, employing a fabricated motorized setup in a microCT, we demonstrate that the fibrous network structure with... Read more

Gili R. S. Naveh, Jonathan E. Foster, Tomas M. Silva Santisteban, Xianrui Yang, and Bjorn R. Olsen

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Functional Electrical Stimulation Leads to Increased Volume of the Aged Thyroarytenoid Muscle

Functional Electrical Stimulation Leads to Increased Volume of the Aged Thyroarytenoid Muscle

A stimulation electrode was placed unilaterally near the terminal adduction branch of the recurrent laryngeal nerve (RLN) adjacent to the right cricothyroid joint. The electrode was connected to an implant located subcutaneously at the neck region. Predesigned training patterns were automatically delivered by a bidirectional radio frequency link using a programming device and were repeated automatically by the implant every other day over 11 weeks in the awake animal. Outcome parameters compr... Read more

Markus Gugatschka, MD, DMSci, Jonathan C. Jarvis, PhD, Justin D. Perkins, MSc, Vladimir Bubalo, PhD, Iris Wiederstein-Grasser, PhD, Hermann Lanmüller, PhD, Claus Gerstenberger, MSc and Michael Karbiener, PhD

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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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New omomyoids (Euprimates, Mammalia) from the late Uintan of southern California, USA, and the question of the extinction of the Paromomyidae (Plesiadapiformes, Primates)

New omomyoids (Euprimates, Mammalia) from the late Uintan of southern California, USA, and the question of the extinction of the Paromomyidae (Plesiadapiformes, Primates)

Paromomyidae has been thought to represent the longest-lived group of stem primates (plesiadapiforms), extending from the early Paleocene to late Eocene. We analyzed primate material from the late-middle Eocene of southern California that had initially been ascribed to cf. Phenacolemur shifrae. This material falls at the lowest end of the size range for the family. The Californian specimens also exhibit several dental features that are atypical for paromomyids, such as a strong paraconid on t... Read more

Sergi López-Torres, Mary T. Silcox, and Patricia A. Holroyd

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Two-fluid model to simulate metal powder bed fusion additive manufacturing

Two-fluid model to simulate metal powder bed fusion additive manufacturing

This paper reports our simulations of the metal powder fusion additive manufacturing process based on a two-fluid model. In simulations of metal behavior in which heat is applied by high-density energy sources (e.g., laser or electron beam), the aspects that need to be correctly modeled include boiling and evaporation, as well as melting and solidification. The potential of the two-fluid model to clarify numerous physical phenomena—deep penetration, plume generation, spatter generation due ... Read more

Noriko WATARI, Yuzuru OGURA, Noriko YAMAZAKI, Yukihiko INOUE, Keisuke KAMITANI, Yasuyuki FUJIYA, Masahiko TOYODA, Saneyuki GOYA, Toshiya WATANABE

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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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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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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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