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.

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.

Evolutionary radiation of earless frogs in the Andes: molecular phylogenetics and habitat shifts in high-elevation terrestrial breeding frogs

The loss of hearing structures and loss of advertisement calls in many terrestrial breeding frogs (Strabomantidae) living at high elevations in South America are common and intriguing phenomena. The Andean frog genus Phrynopus Peters, 1873 has undergone an evolutionary radiation in which most species lack the tympanic membrane and tympanic annulus, yet the phylogenetic relationships among species in this group remain largely unknown. Here, we present an expanded molecular phylogeny of ...

May R, Lehr E, Rabosky DL. PeerJ 6:e4313

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X-ray computed tomography of packed bed chromatography columns for three dimensional imaging and analysis

Physical characteristics critical to chromatography including geometric porosity and tortuosity within the packed column were analysed based upon three dimensional reconstructions of bed structure in-situ. Image acquisition was performed using two X-ray computed tomography systems, with optimisation of column imaging performed for each sample in order to produce three dimensional representations of packed beds at 3 μm resolution.

Department of Biochemical Engineering, University College London | Pall Life Sciences, Portsmouth | Electrochemical Innovation Lab, Department of Chemical Engineering, University College London

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A multi-scale correlative investigation of ductile fracture

The use of novel multi-scale correlative methods, which involve the coordinated characterization of matter across a range of length scales, are becoming of increasing value to materials scientists. Here, we describe for the first time how a multi-scale correlative approach can be used to investigate the nature of ductile fracture in metals. Specimens of a nuclear pressure vessel steel, SA508 Grade 3, are examined following ductile fracture using medium and high-resolution 3D X-ray computed tomog...

School of Materials, University of Manchester; National Nuclear Laboratory; BAM Federal Institute for Materials Research and Testing; Thermo Fischer Scientific

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Fragmentation of wall rock garnets during deep crustal earthquakes

Deformation of the lithosphere by seismic slip along faults dissipates energy to the immediate surroundings as heat and elastic waves. Heat effects may occasionally cause frictional melting along the slip plane, leading to the formation of pseudotachylite, a characteristic fine-grained or glassy fault rock, interpreted as the quenched melt. Recently, it has been suggested that mechanical effects due to rapid loading, such as the formation of shiny “mirror” surfaces or pulverization of rocks ...

Department of Geosciences, University of Oslo; Department of Earth Sciences, Utrecht University; Géosciences Montpellier, Université de Montpellier; Debye Institute for Nanomaterials Science, Utrecht University

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Characterization of 3D fracture evolution in concrete using in-situ X-Ray Computed Tomography testing and Digital Volume Correlation

X-ray Computed Tomography (XCT) is a powerful technology that can accurately image the internal structures of composite and heterogeneous materials in three-dimensions (3D). In this study, in-situ micro XCT tests of concrete specimens under progressive compressive loading are carried out. The aim of the observations is to gain a better understanding of 3D fracture and failure mechanisms at the meso-scale. To characterise the fracture evolution as the deformation increases, two methods are used. ...

College of Civil Engineering and Architecture, Zhejiang University | School of Mechanical, Aerospace and Civil Engineering, the University of Manchester | Manchester X-ray Imaging Facility | Oxford Martin School and Department of Materials

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Experimental study on the cracking process of layered shale using X-ray microCT

The cracking process in Longmaxi formation shale was experimentally studied during uniaxial compressive loading. Both the evolution of the three-dimensional fracture network and the micromechanics of failure in the layered shale were examined as a function of the inclination angle of the bedding plane. To visualize the cracking process, the test devices presented here used an industrial X-ray CT scanner that enabled scanning during the uniaxial compressive loading. Scanning electron microscopy a...

Institue of Geomechanic, Chinese Academy of Geological Sciences, Laboratory of Shale Oil & Gas, Beijing, China

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High-Resolution 3D FIB-SEM Image Analysis and Validation of Numerical Simulations of Nanometre-Scale Porous Ceramic with Comparisons to Experimental Results

The development of focused ion beam-scanning electron microscopy (FIB-SEM) techniques has allowed high-resolution 3D imaging of nanometre-scale porous materials. These systems are of important interest to the oil and gas sector, as well as for the safe long-term storage of carbon and nuclear waste. This work focuses on validating the accurate representation of sample pore space in FIB-SEM-reconstructed volumes and the predicted permeability of these systems from subsequent single-phase flow simu...

Department of Chemical Engineering, Qatar Carbonates and Carbon Storage Research Centre, Imperial College London | Department of Applied Mathematics and Theoretical Physics, Cambridge University

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Hydraulic properties of porous sintered glass bead systems

In this paper, porous sintered glass bead packings are studied, using X-ray Computed Tomography (XRCT) images at  University of Twente, Enschede | Ruhr-University Bochum; Eindhoven University of Technology | Helmholtz Institute Erlangen-Nürnberg for Renewable Energy | University of Stuttgart

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The Manufacturing Technology Centre (MTC) uses Avizo to quantify potential defects in additively manufactured samples

Electron Beam Melting (EBM) is an Additive Manufacturing (AM) process which can be used to fabricate complex 3D metal components. Ti-6Al-4V is one of the high value aerospace materials that has been widely used in the EBM process. However, defects such as gas pores and lack of fusion are often found in the as-built components, which can make a significant difference to the fatigue resistance of the parts. The Manufacturing Technology Centre (MTC) uses X-ray Computed Tomography (XCT) and 3D image...

Dr Shuai Hou, Mélanie Bombardiere, Nathanael Turner, Jonathan Settle, Emmanuel Muzangaza, Dr David Brackett

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Paleozoic Nymphal Wing Pads Support Dual Model of Insect Wing Origins

The appearance of wings in insects, early in their evolution [1], has been one of the more critical innovations contributing to their extraordinary diversity. Despite the conspicuousness and importance of wings, the origin of these structures has been difficult to resolve and represented one of the “abominable mysteries” in evolutionary biology [2]. More than a century of debate has boiled the matter down to two competing alternatives—one of wings representing an extension of the thoracic ...

Department of Zoology, Faculty of Science, Charles University, Praha, Czech Republic and al.

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The NOVA project: maximizing beam time efficiency through synergistic analyses of SRµCT data

Beamtime and resulting SRμCT data are a valuable resource for researchers of a broad scientific community in life sciences. Most research groups, however, are only interested in a specific organ and use only a fraction of their data. The rest of the data usually remains untapped. By using a new collaborative approach, the NOVA project (Network for Online Visualization and synergistic Analysis of tomographic data) aims to demonstrate, that more efficient use of the valuable beam time is possible...

The international society for optics and photonics (SPIE)

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A virtual world of paleontology


Computer-aided visualization and analysis has revolutionized the study of fossils. Fossils can now be characterized in three dimensions and in unprecedented detail. The resulting digital reconstructions can be used in rigorous functional analyses. Hypotheses regarding the function of extinct organisms can therefore be tested.  

Trends in Ecology & Evolution

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X-ray tomographic imaging of tensile deformation modes of electrospun biodegradable polyester fibers

Electrospinning allows the production of fibrous networks for tissue engineering, drug delivery, and wound healing in health care. It enables the production of constructs with large surface area and a fibrous morphology that closely resembles the extracellular matrix of many tissues. A fibrous structure not only promotes cell attachment and tissue formation but could also lead to very interesting mechanical properties. Poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P(3HB-co-4HB)) is a biodegradab...

Jekaterina Maksimcuka, Akiko Obata, William W. Sampson, Remi Blanc, Chunxia Gao, Philip J. Withers, Olga Tsigkou, Toshihiro Kasuga, Peter D. Lee, Gowsihan Poologasundarampillai

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Contrast-enhanced 3D micro-CT of plant tissues using different impregnation techniques

X-ray micro-CT has increasingly been used for 3D imaging of plant structures. At the micrometer reso-lution however, limitations in X-ray contrast often lead to datasets with poor qualitative and quantitative measures, especially within dense cell clusters of plant tissue specimens. The current study developed protocols for delivering a cesium based contrast enhancing solution to varying plant tissue specimens for the purpose of improving 3D tissue structure characterization within plant specime...

Zi Wang, Pieter Verboven and Bart Nicolai, Department of Biosystems KU Leuven – University of Leuven Willem de Croylaan, Leuven Belgium

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X-ray tomography-assisted study of a phase inversion process in ceramic hollow fiber systems – Towards practical structural design

In this study, a series of alumina hollow fibers have been prepared with varied polymer binder (polyethersulfone, PESf) concentration and new polymer-based internal coagulant (aqueous solution of polyvinyl alcohol, PVA). For the first time, the micro-channels were characterized in 3D using X-ray CT to determine micro-channel densities and diameters in the radial direction, as well as the 2D measurement of the pore size in the sponge-like layer.

Tao Li, Xuekun Lu, Bo Wang, Zhentao Wu, Kang Li, Dan J.L. Brett, Paul R. Shearing

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Multi-length scale tomography for the determination and optimization of the effective microstructural properties in novel hierarchical solid oxide fuel cell anodes

Our parametric study shows that increasing the porosity in the spongy layer beyond 10% enhances the effective transport parameters of the spongy layer at an exponential rate, but linearly for the full anode. For the first time, local and global mass transport properties are correlated to the microstructure, which is of wide interest for rationalizing the design optimization of SOFC electrodes and more generally for hierarchical materials in batteries and membranes.

Xuekun Lu, Oluwadamilola O. Taiwo, Antonio Bertei, Tao Li, Kang Li, Dan J.L. Brett, Paul R.Shearing

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Durable and self-hydrating tungsten carbide-based composite polymer electrolyte membrane fuel cells

Proton conductivity of the polymer electrolyte membranes in fuel cells dictates their performance and requires sufficient water management. Here, we report a simple, scalable method to produce well-dispersed transition metal carbide nanoparticles. We demonstrate that these, when added as an additive to the proton exchange Nafion membrane, provide significant enhancement in power density and durability over 100 hours, surpassing both the baseline Nafion and platinum-containing recast Nafion mem...

Weiqing Zheng, Liang Wang, Fei Deng, Stephen A. Giles, Ajay K. Prasad, Suresh G. Advani, Yushan Yan & Dionisios G. Vlachos

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Tortuosity in electrochemical devices: a review of calculation approaches

Here, a review of tortuosity calculation procedures applied in the field of electrochemical devices is presented to better understand the resulting values presented in the literature. Visible differences between calculation methods are observed, especially when using porosity–tortuosity relationships and when comparing geometric and flux-based tortuosity calculation approaches.

Bernhard Tjaden, Dan J. L. Brett, Paul R. Shearing

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Improving microstructural quantification in FIB/SEM nanotomography

Advanced nanotomographic analysis is still far from routine, and a number of challenges remain in data acquisition and post-processing. In this work, we present a number of techniques to improve the quality of the acquired data, together with easy-to-implement methods to obtain “advanced” microstructural quantifications. The techniques are applied to a solid oxide fuel cell cathode of interest to the electrochemistry community, but the methodologies are easily adaptable to a wide range of ma...

Joshua A.Taillon, Christopher Pellegrinelli, Yi-Lin Huang, Eric D.Wachsman, Lourdes G. Salamanca-Riba

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Morphological evolution and internal strain mapping of pomelo peel using X-ray computed tomography and digital volume correlation

Among natural cellular materials, pomelo peels, having a foam-like hierarchical microstructure, represent an ideal model for developing materials with high energy absorption efficiency. In this work, by combining X-ray tomographic imaging technique and digital volume correlation (DVC), in-situ stepwise uniaxial compression tests were performed to quantify the internal morphological evolution and kinematic responses of pomelo peel samples during compression.

B.Wang, B.Pan, G.Lubineau

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Exploring hominin and non-hominin primate dental fossil remains with neutron microtomography

Fossil dental remains are an archive of unique information for paleobiological studies. Computed microtomography based on Xray microfocus sources (X-µCT) and Synchrotron Radiation (SR-µCT) allow subtle quantification at the micron and sub-micron scale of the meso- and microstructural signature imprinted in the mineralized tissues, such as enamel and dentine, through highresolution “virtual histology”. Nonetheless, depending on the degree of alterations undergone during fossilizatio...

Clément Zanolli, Laboratory AMIS, UMR 5288, University of Toulouse III - Paul Sabatier, France, and al.

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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.

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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Correlation between triple phase boundary and the microstructure of Solid Oxide Fuel Cell anodes

This study aims to correlate the active triple phase boundaries (TPBs) to the variation of as-prepared anode microstructures and Ni densifications based on the reconstructed 3D volume of an SOFC anode, providing a point of comparison with theoretical studies that reveal the relationship of TPBs and the material microstructure using randomly packed spheres models.

Xuekun Lu, Thomas M.M. Heenan, Josh J. Bailey, Tao Li, Kang Li, Daniel J.L. Brett, Paul R. Shearing, Electrochemical Innovation Lab, Department of Chemical Engineering, University College London, London

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Revealing the skeleton of polar dinosaur using synchrotron computed tomography

Leaellynasaura amicagraphica was a small, bipedal, herbivorous dinosaur from the Early Cretaceous (~106 million years ago) of Australia within the Antarctic Circle of that time. Synchrotron scans, and the resulting 3D reconstruction of the skull and post-cranial skeleton, provide a unique view of the morphology of Leaellynasaura, and allows this material to be 3D printed for display.

1University College London, UK; Monash University, Melbourne, Australia; Museum Victoria, Melbourne, Australia

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Scientists discover the oldest Homo sapiens fossils at Jebel Irhoud, Morocco

New finds of fossils and stone tools from the archaeological site of Jebel Irhoud, Morocco, push back the origins of our species by one hundred thousand years and show that by about 300 thousand years ago important changes in our biology and behaviour had taken place across most of Africa.

Max Planck Institute for Evolutionary Anthropology (Leipzig, Germany)

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2 BILLION years old fossils appear to represent a first experiment in megascopic multicellularity

The Paleoproterozoic Era witnessed crucial steps in the evolution of Earth’s surface environments following the first appreciable rise of free atmospheric oxygen concentrations ∼2.3 to 2.1 Ga ago, and concomitant shallow ocean oxygenation. Combined microtomography, geochemistry, and sedimentary analysis suggest a biota fossilized during early diagenesis. The emergence of this biota follows a rise in atmospheric oxygen, which is consistent with the idea that surface oxygenation allowed t...

Abderrazak El Albani, Laboratoire HYDRASA, UMR 6269 CNRS-INSU, Université de Poitiers, France

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L4iS uses Avizo software to analyze 3D images from laser ablation tomography

Lasers for Innovative Solutions, LLC (L4iS) is developing a new class of tomography technology with the aim of allowing material characterization in three dimensions with sub-micron resolution. The method uses a nanosecond, Q-switched, pulsed ultraviolet laser coupled with high-resolution imaging to generate highly detailed specimen models. Using this system, sequential images similar to light-sheet fluorescence microscopy are used to digitally reconstruct the specimen.

Brian Reinhardt and Benjamin Hall, L4iS (USA)

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FAMU uses Avizo software to visualize and understand heat transfer and fluid flow

The CHEFF (Computational Heat Fluid Flow) Research group at Florida Agricultural & Mechanical University is using computational fluid dynamics to model flow and heat transfer in various engineering applications for industry, government and the private sector. The primary goal of this research is to first examine and then enhance the thermal performance of current and future low-density reticulated porous media, and explore their use as heat sinks in high power electronics (computer chips), ...

CHEFF Research Group at Florida Agricultural & Mechanical University: Dr. G.D. Wesson, Professor of Chemical Engineering/Biological Agricultural Systems Engineering, Shawn Austin (Graduate student), Shari Briggs (Graduate student), Mellissa McCole (Graduate student), David Mosley (Graduate student)

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The University of Birmingham uses Avizo software to explore the North Sea as it was 10,000 years ago

The IBM Visual and Spatial Technology Centre (VISTA) specialize in large scale data capture, analysis and visualization for the Arts and Humanities at the University of Birmingham, UK. The VISTA Centre supports interdisciplinary academic research and application development for visualization, spatial analysis and imaging using state-ofthe- art technology. Avizo software is a fundamental tool that provides new opportunities for data comprehen...

IBM Visual and Spatial Technology Centre, Institute of Archaeology, Birmingham Archaeology, University of Birmingham, UK

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University of Glasgow uses Amira software to analyze vascular structures

The vascular (arterial or venous) wall is a fascinating structure. At the simplest level, we can think of the wall as being composed of three distinct, but interacting, layers . The vascular wall changes its structure in conditions such as hypertension which can cause a thickening of the wall. Unfortunately, the details of this ‘remodeling’ process are poorly understood. Therefore, studying the 3D architecture may provide vital clues for future therapeutic targets. Researcher at the ...

Dr. Craig J Daly, School of Life Sciences, College of Medical Veterinary & Life Sciences, University of Glasgow

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KTH Royal Institute of Technology uses Avizo software to visualize and characterize the internal structure of civil engineering materials

The Division of Highway and Railway Engineering, Royal Institute of Technology (KTH) promotes advances in computational and experimental science in order to develop new materials, tools and systems for improved mobility, transportation safety and infrastructure durability. The group works on analysis and performance-based design of roads and tracks, management as well as operation and maintenance of roads.

Denis Jelagin, Alvaro Guarin, Ibrahim Onifade, Nicole Kringos, and Bjorn Birgisson (KTH)

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SIK-ISEA uses Avizo software to understand 19th century painting techniques

The characterization of the porosity of ground layers in easel paintings: a first step towards understanding its role in water uptake, reactivity and material transport in 19th and early 20th century paintings. The Swiss Institute for Art Research (SIK-ISEA) is studying the studio practice of Swiss painters of the late 19th early 20th century, the materials they used for their paintings, and the deterioration processes the paintings undergo as they age. Amongst other issues this study is lookin...


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Utilization of longitudinal ultrasound to quantify joint soft-tissue changes in a mouse model of posttraumatic osteoarthritis

Ultrasound could be a fast and cost-effective means of assessing joint changes in mouse models of posttraumatic osteoarthritis (PTOA). Such models are essential for understanding the biology of this degenerative joint disease and developing new treatments, but noninvasive methods of evaluating disease activity are lacking. Because ultrasound can visualize both joint space volumes and blood flow in the joints, it could provide an alternative to microscopic examination of tissue, assuming it accur...

Hao Xu, Echoe M Bouta, Ronald W Wood, Edward M Schwarz, Yongjun Wang & Lianping Xing

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Human liver segments: role of cryptic liver lobes and vascular physiology in the development of liver veins and left-right asymmetry

Couinaud based his well-known subdivision of the liver into (surgical) segments on the branching order of portal veins and the location of hepatic veins. However, both segment boundaries and number remain controversial due to an incomplete understanding of the role of liver lobes and vascular physiology on hepatic venous development. Human embryonic livers (5–10 weeks of development) were visualized with Amira 3D-reconstruction and Cinema 4D-remodeling software.

Jill P. J. M. Hikspoors, Mathijs M. J. P. Peeters, Nutmethee Kruepunga, Hayelom K. Mekonen, Greet M. C. Mommen, S. Eleonore Köhler & Wouter H. Lamers

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Cytoplasmic and Nuclear Retained DMPK mRNAs Are Targets for RNA Interference in Myotonic Dystrophy Cells

This paper demonstrates for the first time down-regulation of the endogenous nuclear retained mutant DMPK mRNAs targeted with lentivirus-delivered short hairpin RNAs (shRNAs). This nuclear RNAi(-like) phenomenon was not observed when synthetic siRNAs were delivered by cationic lipids, suggesting either a link between processing of the shRNA and nuclear import or a separate pathway for processing shRNAs in the nuclei.

Marc-André Langlois,  Christelle Boniface,  Gang Wang,  Jessica Alluin, Paul M. Salvaterra,  Jack Puymirat,  John J. Rossi, Nan Sook Lee

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University of Washington researchers use Amira software towards aiding the pathology of pancreatic cancer

For nearly 100 years, pathology for cancer diagnosis has involved a standard, but complex series of steps to process tissue biopsies procured from a patient in the clinic. Many procedures are a direct result of the fact that observation and evaluation of specimens by pathologists occur using a standard microscope (in 2D). In 2014, the Human Photonics Laboratory at the University of Washington demonstrated that the rudimentary operations of a pathology laboratory may be replicated on whole, unsec...

Ronnie Das, PhD and Eric J. Seibel, PhD

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UCSF School of Dentistry uses Avizo software to extract changes in periodontal ligament space and tooth movement due to orthodontic therapy

During the acts of biting and chewing, the muscles of the jaw (consisting of the masseter, temporalis, and medial pterygoid in the elevator group, and lateral pterygoid as the main depressor) generate forces that dictate jaw kinematics . The movement of jaws hinges about the temporomandibular joint and are brought together by the muscles attached to respective bones through bone-tendon interfaces known as entheses . Thus, chewing forces affect aspects of craniofacial structure as well as bone ...

Kyle H.-Y. Chan, fourth-year undergraduate student in Molecular and Cell Biology, and Public Health at UC Berkeley, FeiFei Yang, Ph.D., postdoctoral scholar in the Laboratory of Multiscale Biomechanics and Biomineralization, School of Dentistry, UCSF, and Sunita P. Ho, Ph.D., Division of Biomaterials and Bioengineering, Department of Preventive and Restorative Dental Sciences, School of Dentistry, University of California San Francisco

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The Brazilian Synchrotron Light Laboratory (LNLS) uses Avizo to visualize and analyze scientific and industrial 3D data acquired with their X-Ray Imaging Beamline (IMX)

The imaging beamline, IMX, at LNLS extracts synchrotron radiation from bending magnet D6 with magnetic field of 1.67 T and bending radius of 2.736 m. It has an electron source size of 391  Brazilian Synchotron Light Laboratory

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The Oriental Institute of the University of Chicago uses Amira sotware to visualize and analyze Egyptian mummified birds

Entering this special exhibit at the Oriental Institute Museum at the University of Chicago, you will immediately feel transported into the ancient  Nile delta marshlands with its lush green flora. The combination of colors, video footage, bird songs, and ancient artifacts will give you the impression that you have just traveled through time and space. At the start of the exhibit, you will find one of their most impressive artifacts, an empty shell of an ostrich egg from 3100 B.C. With its perf...

Rozenn Bailleul-LeSuer, The University of Chicago, Department of Near Eastern Languages and Civilizations

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AMSC Research, LLC uses Amira software to understand processes and rituals of Egyptian mummification

“Scanning is important, but it is really just the first step in an immersive exploration of artifacts” says Elias. Raw data from scans taken of mummies (or other archaeological subject matter) is delivered to AMSC Research as files in a language known as DICOM. Next, these are converted into a visually readable form for analytical purposes and to launch the creative modeling process. Elias uses Amira software to analyze scan data. Mummies are biological entities, so apart from the us...

Dr. Jonathan Elias, AMSC Research, LLC

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The London Centre for Nanotechnology uses Avizo Software to reveal structure of human chromosomes and nucleus in 3D

A team led by London Centre for Nanotechnology researchers, Prof. Ian Robinson and Dr. Bo Chen (now a professor at the Tongji University, Shanghai) used newly-developed serial block-face scanning electron microscopy (SBFSEM) and Thermo Scientific™ Avizo® Software, one dominant tool in 3D reconstructed image processing, to reveal the spatial structure of human chromosomes and nucleus quantitatively at high resolution of approximately 50 nm in three dimensions.

Prof. Ian Robinson, Dr. Bo Chen, London Centre for Nechnology, UCL and Tongji University

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A correlative approach for combining microCT, light and transmission electron microscopy in a single 3D scenario

In biomedical research, a huge variety of different techniques is currently available for the structural examination of small specimens, including conventional light microscopy (LM), transmission electron microscopy (TEM), confocal laser scanning microscopy (CLSM), microscopic X-ray computed tomography (microCT), and many others. Since every imaging method is physically limited by certain parameters, a correlative use of complementary methods often yields a significant broader range of informati...

Stephan Handschuh, Natalie Baeumler, Thomas Schwaha and Bernhard Ruthensteiner

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GEVES uses Avizo software to study and control plant seeds

At GEVES, Microtomography (micro-CT), which is a technique using X-rays to investigate internal anatomy and morphology of organisms without destruction, is applied to plant seed quality control and phenotyping. Several applications have been developed using micro-CT coupled with Avizo software development, such as for example in the Measurements of internal and external sugar beet seed structures for seed phenotyping

Ghassen Trigui, Laurence Le Corre, Dominique Honoré and Karima Boudehri-Giresse - 2D/3D Imaging - R&D team, GEVES

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Unilever uses Avizo software to visualize and understand food and detergent structures

Food and detergent products are composed of complex micro structures. With modern microscopic techniques we can make them visible. The microstructure greatly affects macroscopic properties such as appearance, taste, mouth feel and solubility. Making these structures visible and quantifying them is essential to the development of products with optimal product properties. A broad range of imaging techniques is used to visualize microstructure elements at different length scales. For example, X-ray...

Gerard van Dalen, Unilever R&D Vlaardingen (The Netherlands)

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UZ Leuven uses Amira software for postoperative evaluation of orthognathic patients

The department of Oral and Maxillofacial Surgery (OMFS) of Leuven University Hospitals (Belgium) is a tertiary referral centre with a strong focus on omfs-resident training, education of dental students and scientific research. Clinical pillars are head and neck oncology, cleft lip and palate, facial deformities, orthognathic surgery, chronic facial pain, severe trauma, maxillofacial imaging and dental oral cripples.

Dr. Ir. Eman SHAHEEN, BSc, MSc, PhD, Responsible of the 3D orthognathic surgical lab, Department of Oral and Maxillo-facial Surgery - UZ Leuven - Belgium

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The Academic Medical Center (AMC) uses Amira to build a 3D Atlas for Human Embryology

The 3D Atlas of Human Embryology project was funded by the Academic Medical Center (AMC) in Amsterdam, the Netherlands, in 2009. Since then, over 75 students, under the supervision of embryologists of the Department of Anatomy, Embryology & Physiology, have contributed to this labor-intens...

Academic Medical Center

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The Max Planck Institute of Neurobiology uses Amira software for axon tracing from head to toe

Ali Ertürk and his collaborators described a novel histo-chemical technique to clear spinal cord tissue of adult mice for fluorescence microscopy imaging of the intact spinal cord. Previously, the high lipid content of the spinal cord tissue in adult mice allowed imaging of the spinal cord only through destructive histological methods, making the tracing of complete axons impossible. As applied in this study, the improved histo-chemistry enabled Ertürk and his colleagues to show that not only ...

Ali Ertürk, Christoph P Mauch, Farida Hellal, Friedrich Förstner, Tara Keck, Klaus Becker, Nina Jährling, Heinz Steffens, Melanie Richter, Mark Hübener, Edgar Kramer, Frank Kirchhoff, Hans Ulrich Dodt & Frank Bradke

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Severe hearing loss and outer hair cell death in homozygous Foxo3 knockout mice after moderate noise exposure

Noise induced hearing loss (NIHL) is a disease that affects millions of Americans. Identifying genetic pathways that influence recovery from noise exposure is an important step forward in understanding NIHL. The transcription factor Foxo3 integrates the cellular response to oxidative stress and plays a role in extending lifespan in many organisms, including humans. Here we show that Foxo3 is required for auditory function after noise exposure in a mouse model system, measured by ABR…

Felicia Gilels, Stephen T. Paquette, Holly J. Beaulac, Anwen Bullen & Patricia M. White

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Reversible silencing of lumbar spinal interneurons unmasks a task-specific network for securing hindlimb alternation

Neural circuitry in the lumbar spinal cord governs two principal features of locomotion, rhythm and pattern, which reflect intra- and interlimb movement. These features are functionally organized into a hierarchy that precisely controls stepping in a stereotypic, speed-dependent fashion. Here, we show that a specific component of the locomotor pattern can be independently manipulated…

Amanda M. Pocratsky, Darlene A. Burke, Johnny R. Morehouse, Jason E. Beare, Amberly S. Riegler, Pantelis Tsoulfas, Gregory J. R. States, Scott R. Whittemore & David S. K. Magnuson

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Biofilm three-dimensional architecture influences in situ pH distribution pattern on the human enamel surface

Acidic microenvironments created by bacterial clusters thriving in a polysaccharide matrix could be behind localized tooth decay. Jin Xiao of the University of Rochester Medical Center and Geelsu Hwang of the University of Pennsylvania with colleagues in the US mapped acidity changes across tooth enamel caused by the microstructure of dental plaque: a film of bacteria and the polysaccharide matrix they secrete. Using fluorescence microscopy, they studied the 3D architecture of plaque that formed...

Jin Xiao, Anderson T Hara, Dongyeop Kim, Domenick T Zero, Hyun Koo et al.

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Morphological process of podocyte development revealed by block-face scanning electron microscopy

Podocytes present a unique 3D architecture specialized for glomerular filtration. However, several 3D morphological aspects on podocyte development remain partially understood because they are difficult to reveal using conventional scanning electron microscopy (SEM). Here, we adopted serial block-face SEM imaging…

Koichiro Ichimura, Soichiro Kakuta, Yuto Kawasaki, Takayuki Miyaki, Takahiro Nonami, Naoyuki Miyazaki, Tomoyo Nakao, Sakiko Enomoto, Shigeo Arai, Masato Koike, Kazuyoshi Murata, Tatsuo Sakai

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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…

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

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Three-dimensional imaging of the intracellular assembly of a functional viral RNA replicase complex

Positive-strand RNA viruses, which can be devastating pathogens in humans, animals and plants, replicate their genomes on intracellular membranes. Here, we describe the three-dimensional ultrastructural organization of a tombusvirus replicase in yeast, a valuable model for exploring virus–host interactions…

Isabel Fernández de Castro, José J. Fernández, Daniel Barajas, Peter D. Nagy, Cristina Risco

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Fast and precise targeting of single tumor cells in vivo by multimodal correlative microscopy

Intravital microscopy provides dynamic understanding of multiple cell biological processes, but its limited resolution has so far precluded structural analysis. Because it is difficult to capture rare and transient events, only a few attempts have been made to observe specific developmental and pathological processes in animal models using electron microscopy. The multimodal correlative approach that we propose here combines intravital microscopy, microscopic X-ray computed tomography and three-...

Matthia A. Karreman, Luc Mercier, Nicole L. Schieber, Gergely Solecki, Guillaume Allio, Frank Winkler, Bernhard Ruthensteiner, Jacky G. Goetz, Yannick Schwab

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Determining the bacterial cell biology of planctomycetes

Bacteria of the phylum Planctomycetes have been previously reported to possess several features that are typical of eukaryotes, such as cytosolic compartmentalization and endocytosis-like macromolecule uptake. However, recent evidence points towards a Gram-negative cell plan for Planctomycetes, although in-depth experimental analysis has been hampered by insufficient genetic tools…

Christian Boedeker, Margarete Schüler, Greta Reintjes, Olga Jeske, Muriel C. F. van Teeseling et al.

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Macropinosomes are key players in early shigella invasion and vacuolar escape in epithelial cells

Intracellular pathogens include all viruses, many bacteria and parasites capable of invading and surviving within host cells. Key to survival is the subversion of host cell pathways by the pathogen for the purpose of propagation and evading the immune system. The intracellular bacterium Shigella flexneri, the causative agent of bacillary dysentery, invades host cells in a vacuole that is subsequently ruptured to allow growth of the pathogen within the host cytoplasm…

Allon Weiner , Nora Mellouk , Noelia Lopez-Montero , Yuen-Yan Chang, Célia Souque, Christine Schmitt, Jost Enninga

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A global approach for quantitative super resolution and electron microscopy on cryo and epoxy sections using self-labeling protein tags

Correlative light and electron microscopy (CLEM) is a powerful approach to investigate the molecular ultrastructure of labeled cell compartments. However, quantitative CLEM studies are rare, mainly due to small sample sizes and the sensitivity of fluorescent proteins to strong fixatives and contrasting reagents for EM. Here, we show that fusion of…

Andreas Müller, Martin Neukam, Anna Ivanova, Anke Sönmez, Carla Münster, Susanne Kretschmar, Yannis Kalaidzidis, Thomas Kurth, Jean-Marc Verbavatz & Michele Solimena

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Imaging multicellular specimens with real-time optimized tiling light-sheet selective plane illumination microscopy

Despite the progress made in selective plane illumination microscopy, high-resolution 3D live imaging of multicellular specimens remains challenging. Tiling light-sheet selective plane illumination microscopy (TLS-SPIM) with real-time light-sheet optimization was developed to respond to the challenge…

Qinyi Fu, Benjamin L. Martin, David Q. Matus, Liang Gao

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Patterns of organelle ontogeny through a cell cycle revealed by whole-cell reconstructions using 3D electron microscopy

The major mammalian bloodstream form of the African sleeping sickness parasite Trypanosoma bruceimultiplies rapidly, and it is important to understand how these cells divide. Organelle inheritance involves complex spatiotemporal re-arrangements to ensure correct distribution to daughter cells…

Louise Hughes, Samantha Borrett, Katie Towers, Tobias Starborg, Sue Vaughan

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Deep nuclear invaginations are linked to cytoskeletal filaments – integrated bioimaging of epithelial cells in 3D culture

The importance of context in regulation of gene expression is now an accepted principle; yet the mechanism by which the microenvironment communicates with the nucleus and chromatin in healthy tissues is poorly understood. A functional role for nuclear and cytoskeletal architecture is suggested by the phenotypic differences observed between epithelial and mesenchymal cells…

Danielle M. Jorgens, Jamie L. Inman, Michal Wojcik, Claire Robertson, Hildur Palsdottir, Wen-Ting Tsai, Haina Huang, Alexandre Bruni-Cardoso, Claudia S. López, Mina J. Bissell, Ke Xu, Manfred Auer

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Application of nuclear volume measurements to comprehend the cell cycle in root-knot nematode-induced giant cells

Root-knot nematodes induce galls that contain giant-feeding cells harboring multiple enlarged nuclei within the roots of host plants. It is recognized that the cell cycle plays an essential role in the set-up of a peculiar nuclear organization that seemingly steers nematode feeding site induction and development. Functional studies of a large set of cell cycle genes in transgenic lines of the model host Arabidopsis thaliana have contributed to better understand the role of the cell cycle compone...

Antonino de Souza Junior José Dijair, Pierre Olivier, Coelho Roberta R., Grossi-de-Sa Maria F., Engler Gilbert, de Almeida Engler Janice / Institut National de la Recherche Agronomique, Université Côte d’Azur, Centre National de la Recherche Scientifique, Institut Sophia Agrobiotech, Sophia-Antipolis, France

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Glass fiber length and orientation analysis of reinforced polymers (GFRP)

Royal DSM is a global science-based company active in health, nutrition and
materials. Within DSM’s Materials Cluster DSM Engineering Plastics is a global player in specialty plastics. These materials are used in components for the electrical and electronics, automotive, flexible food packaging and consumer goods industries. A typical product made of DSM Engineering Plastics’ polymer portfolio are USB-C connectors. Key performance indicators for this application are dimensional and tem...

Jennifer Schillings, Arno Wilbers and Joachim Loos, DSM Materials Science Center, Geleen, The Netherlands

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