Welcome to the Amira-Avizo Software Use Case Gallery

Progressive transformation of the otic placode into the functional inner ear during gestational development in humans leads to the acquisition of hearing perception via the cochlea and balance and spatial orientation via the vestibular organ.

Using a correlative approach involving micro-computerized tomography (micro-CT), transmission electron microscopy and histological techniques we were able to examine both the morphological and cellular changes associated with human inner ear devel... Read more

In this work, we studied mitochondria-rER contacts in vivo by serial section electron tomography (SSET) and 3D reconstruction analysis of cryo-fixed mouse tissue samples. We characterized this inter-organelle association as mitochondria tightly wrapped by sheets of curved rER (wrappER). Further, we used multi-omics and genetic approaches to obtain evidence that the wrappER is a distinct intracellular compartment and demonstrate the importance of wrappER-mitochondria contacts for v... Read more

Lithium ion battery failure occurs across multiple length scales. In this work, the properties of thermal failure and its effects on electrode materials were investigated in a commercial battery using a combination of accelerating rate calorimetry (ARC) and multi-length scale X-ray computed tomography (CT). ARC measured the heat dissipated from the cell during thermal runaway and enabled the identification of key thermal failure characteristics such as onset temperature and the rate of heat g... Read more

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID19 pandemic, is a highly pathogenic β-coronavirus. As other coronaviruses, SARS-CoV-2 is enveloped, replicates in the cytoplasm and assembles at intracellular membranes. Here, we structurally characterize the viral replication compartment and report critical insights into the budding mechanism of the virus, and the structure of extracellular virions close to their native state by in situ cryo-electr... Read more

Since its invention and commercialization in the 1950s, ultra-high molecular weight polyethylene (UHMWPE) has been known as a high-performance polymer successfully applied in diverse engineering systems ranging from strong ropes for naval demands and wear-resistant liners in bearings, transportation belts and heavy trucks in mines and quarries, through the lining of chemical vessels and disposable bags in bioreactors, to sophisticated products such as orthopaedic implants and replacements of ... Read more

Inconel 718 (IN718) is the most popular precipitation-strengthened nickel-based superalloy introduced by the Huntington Alloys Division of INCO in 1959 (Ref Read more

With the growing use of X-ray computed tomography (X-ray CT) datasets for modelling of transport properties, comes the need to define the representative elementary volume (REV) if considering three dimensions or the representative elementary area (REA) if considering two dimensions. The resolution used for imaging must be suited to the features of interest in the sample and the region-of-interest must be sufficiently large to capture key information. Polymer electrolyte fuel cells have a hier... Read more

A solid oxide fuel cell (SOFC) is an electrochemical device that converts the chemical energy of hydrogen directly into electricity. A single cell usually has a form of a flat plate in which an impervious and dense ion-conducting electrolyte is sandwiched between two porous catalytic electrodes: an anode and a cathode. Fuel is fed to the anode side, and the air is supplied to the cathode. The gasses cannot mix to avoid unproductive combustion. Instead, gasses hit catalyst material, lose their... Read more

Degradation mechanisms within solid oxide fuel cells (SOFC) during thermal cycling limit operational start-up times and cell lifetime, and must therefore be better understood and mitigated. This work explores such mechanisms using digital volume correlation (DVC) techniques applied to lab-based X-ray tomograms where the microstructural evolution is evaluated during the operational cycling of a Ni–YSZ/YSZ cell. To emulate reduced start-up times, five tomograms were collected over four operat... Read more

Lithium sulfur (Li–S) batteries have great potential as a successor to Li-ion batteries, but their commercialization has been complicated by a multitude of issues stemming from their complex multiphase chemistry. In situ X-ray tomography investigations enable direct observations to be made about a battery, providing unprecedented insight into the microstructural evolution of the sulfur cathode and shedding light on the reaction kinetics of the sulfur phase. Here, for the first time, the mor... Read more

The electrode microstructural properties significantly influence the efficiency and durability of many electrochemical devices including solid oxide fuel cells. Despite the possibility of simulating the electrochemical phenomena within real three-dimensional microstructures, the potential of such 3D microstructural information has not yet been fully exploited. We introduce here a completely new methodology for the advanced characterization of inhomogeneous current distribution base... Read more

The importance of reliable battery diagnostic systems has grown substantially in recent years as a result of the use of high power Li-ion battery packs in an increasingly diverse range of applications. Here, spatially resolved ultrasound acoustic measurements are used to analyse the condition of Li-ion electrodes. Ultrasonic measurements are performed on a commercial mobile phone battery over the full operating voltage window with the lithiation and delithiation of electrodes o... Read more

Retroviruses evolved from long terminal repeat (LTR) retrotransposons by acquisition of envelope functions, and subsequently reinvaded host genomes. Together, endogenous retroviruses and LTR retrotransposons represent major components of animal, plant, and fungal genomes. Sequences from these elements have been exapted to perform essential host functions, including placental development, synaptic communication, and transcriptional regulation. They encode a Gag polypeptide, the capsid domains ... Read more

As key functional units in neural circuits, different types of neuronal synapses play distinct roles in brain information processing, learning, and memory. Synaptic abnormalities are believed to underlie various neurological and psychiatric disorders. Here, by combining cryo-electron tomography and cryo-correlative light and electron microscopy, we distinguished intact excitatory and inhibitory synapses of cultured hippocampal neurons, and visualized the in situ 3D organization of ... Read more

Corpora amylacea are cell-derived structures that appear physiologically in the aged human brain. While their histological identification is straightforward, their ultrastructural composition and microenvironment at the nanoscale have remained unclear so far, as has their relevance to aging and certain disease states that involve the sequestration of toxic cellular metabolites. Here, we apply correlative serial block-face scanning electron microscopy and transmission electron tomograp... Read more

A novel archaeal virus, denoted Sulfolobus ellipsoid virus 1 (SEV1), was isolated from an acidic hot spring in Costa Rica. The morphologically unique virion of SEV1 contains a protein capsid with 16 regularly spaced striations and an 11-nm-thick envelope. The capsid exhibits an unusual architecture in which the viral DNA, probably in the form of a nucleoprotein filament, wraps around the longitudinal axis of the virion in... Read more

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.

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…

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…

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…