Welcome to the Amira-Avizo Software Use Case Gallery

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…

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…

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…

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…

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…

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…

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…

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…

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 thr... Read more

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

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.

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... 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.

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 to... Read more

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 use... Read more