Welcome to the Amira-Avizo Software Use Case Gallery

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

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... Read more

Madtsoiids are among the most basal snakes, with a fossil record dating back to the Upper Cretaceous (Cenomanian). Most representatives went extinct by the end of the Eocene, but some survived in Australia until the Late Cenozoic. Yurlunggur and Wonambi are two of these late forms, and also the best-known madtsoiids to date. A better understanding of the anatomy and palaeoecology of these taxa may shed light on the evolution and extinction of this poorly known group of s... Read more

The ∼3.48 billion-year-old Dresser Formation, Pilbara Craton, Western Australia, is a key geological unit for the study of Earth’s earliest life and the habitats it occupied. Here, we describe a new suite of spheroidal to lenticular microstructures that morphologically resemble some previously reported Archean microfossils. Correlative microscopy shows that these objects have a size distribution, wall ultrastructure, and chemistry that are incompatible with a microfossil origin and in... Read more

We demonstrate that phase retrieval and tomographic imaging at the organ level of small animals can be advantageously carried out using the monochromatic radiation emitted by a compact x-ray light source, without further optical elements apart from source and detector. This approach allows to carry out microtomography experiments which – due to the large performance gap with respect to conventional laboratory instruments – so far were usually limited to synchrotron sources. We dem... Read more

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

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…

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…

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

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.

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.

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

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.

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.

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 possi... Read more

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... Read more

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-int... Read more

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... Read more