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

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 spec... Read more

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

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

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 comp... Read more

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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Potential hominin affinities of Graecopithecus from the Late Miocene of Europe

Potential hominin affinities of Graecopithecus from the Late Miocene of Europe

The split of our own clade from the Panini is undocumented in the fossil record. To fill this gap we investigated the dentognathic morphology of Graecopithecus freybergi from Pyrgos Vassilissis (Greece) and cf. Graecopithecus sp. from Azmaka (Bulgaria), using new μCT and 3D reconstructions of the two known specimens. Pyrgos Vassilissis and Azmaka are currently dated to the early Messinian at 7.175 Ma and 7.24 Ma. Mainly based on its external preservation and the previou... Read more

Jochen Fuss, Nikolai Spassov, David R. Begun, Madelaine Böhme

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Echoes from the past: New insights into the early hominin cochlea from a phylo-morphometric approach

Echoes from the past: New insights into the early hominin cochlea from a phylo-morphometric approach

Investigation on cochlear variation, an indirect evidence of auditory capacities among early hominins and extant catarrhine species, in order to assess (i) the phylogenetic signal of relative external cochlear length (RECL) and oval window area (OWA), the evolutionary model with the highest probability of explaining our observed data, some hominin ancestral nodes for RECL and OWA. RECL has a high phylogenetic signal under a Brownian motion model, and is closely correlated with body mass. Our... Read more

José Braga, Priscille Bouvier, Jordan Romeyer Dherbey, Patricia Balaresque, Laurent Risser , Jean-Michel Loubes , Jean Dumoncel , Benjamin Duployer , Christophe Tenailleau

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MIA-Clustering: a novel method for segmentation of paleontological material

MIA-Clustering: a novel method for segmentation of paleontological material

Paleontological research increasingly uses high-resolution micro-computed tomography (μCT) to study the inner architecture of modern and fossil bone material to answer important questions regarding vertebrate evolution. This non-destructive method allows for the measurement of otherwise inaccessible morphology. Digital measurement is predicated on the accurate segmentation of modern or fossilized bone from other structures imaged in μCT scans, as errors in segmentation can result in inaccur... Read more

Christopher J. Dunmore​, Gert Wollny, Matthew M. Skinner

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A new ankylosaurine dinosaur from the Judith River Formation of Montana, USA, based on an exceptional skeleton with soft tissue preservation

A new ankylosaurine dinosaur from the Judith River Formation of Montana, USA, based on an exceptional skeleton with soft tissue preservation

The terrestrial Judith River Formation of northern Montana was deposited over an approximately 4 Myr interval during the Campanian (Late Cretaceous). Despite having been prospected and collected continuously by palaeontologists for over a century, few relatively complete dinosaur skeletons have been recovered from this unit to date. Here we describe a new genus and species of ankylosaurine dinosaur, Zuul crurivastator, from the Coal Ridge Member of the Judith River Formation, based ... Read more

Victoria M. Arbour, David C. Evans

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Enhanced Imaging of Lithium Ion Battery Electrode Materials

Enhanced Imaging of Lithium Ion Battery Electrode Materials

The authors present for the first time a new methodology of contrast enhancement for 3D imaging, including novel advanced quantification, on a commercial Lithium Iron Phosphate (LFP) LiFePO4 cathode. The aim of this work is to improve the quality of the 3D imaging of challenging battery materials by developing methods to increase contrast between otherwise previously poorly differentiated phases. This is necessary to enable capture of the real geometry of electrode microstructures... Read more

Moshiel Biton, Vladimir Yufit, Farid Tariq, Masashi Kishimoto and Nigel Brandon

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

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 for... Read more

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

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

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…Read more

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

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

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 ac... Read more

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

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Hydraulic properties of porous sintered glass bead systems

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 16μm16μm voxel resolution, to obtain not only the porosity field, but also other properties like particle sizes, pore throats and the permeability. The influence of the sintering procedure and the original particle size distributions on the microstructure, and thus on the hydraulic properties, is analyzed in detail. The XRCT data are visualized and studied by advanced image fil... Read more

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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