Welcome to the Amira-Avizo Software Use Case Gallery

In recent years new methodologies and workflow pipelines for acquiring correlated fluorescence microscopy and volume electron microscopy datasets have been extensively described and made accessible to users of different levels. Post-acquisition image processing, and particularly correlation of the optical and electron data in a single integrated three-dimensional framework can be key for extracting valuable information, especially when imaging large sample volumes such as whole cells or tissu... Read more

The internal skeleton of the nasal cavity is sporadically and often incompletely described for many marsupial species and mammals in general. Here, I provide an anatomical survey of the ethmoid in the skulls of adult marsupials based on examination of computed tomography (CT) imagery of 29 taxa representing all the major extant groups of marsupials. (…) I compared ecological data with the number of ecto- and endoturbinals as a preliminary test to determine whether some of the interspec... 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.

X-ray computed tomography (X-ray CT) across multiple length scales is utilized for the first time to investigate the physical abuse of high C-rate pulsed discharge on cells wired individually and in parallel.. Manufactured lithium iron phosphate cells boasting high rate capability were pulse power tested in both wiring conditions with high discharge currents of 10C for a high number of cycles (up to 1200) until end of life (<80% of initial discharge capacity retained). The parallel ass... Read more

SiC-SiC ceramic matrix composites are candidate materials for fuel cladding in Generation IV nuclear fission reactors and as accident tolerant fuel clad in current generation plant.

Experimental methods are needed that can detect and quantify the development of mechanical damage, to support modelling and qualification tests for these critical components. In situ observations of damage development have been obtained of tensile and C-ring mechanical test specimens of a braided nuclear gr... Read more

We demonstrate feasibility of the workflow by combining in vivo 2-photon microscopy and focused ion beam scanning electron microscopy (FIB/SEM) to dissect the role of astrocytic coverage in the persistence of dendritic spines.

Emerging 3D correlative light and electron microscopy (CLEM) approaches enable studying neuronal structure-function relations at unprecedented depth and precision. However, established protocols for the correlation of light and electron micrographs rely ... Read more

Precise methods for quantifying drug accumulation in brain tissue are currently very limited, challenging the development of new therapeutics for brain disorders. Transcardial perfusion is instrumental for removing the intravascular fraction of an injected compound, thereby allowing for ex vivo assessment of extravasation into the brain. However, pathological remodeling of tissue microenvironment can affect the efficiency of transcardial perfusion, which has been largely overlooked.

We... Read more

Deep brain stimulation (DBS) requires accurate localization of the anatomical target structure, and the precise placement of the DBS electrode within it. Ultra-high field 7 Tesla (T) MR images can be utilized to create patient-specific anatomical 3D models of the subthalamic nuclei (STN) to enhance pre-surgical DBS targeting as well as post-surgical visualization of the DBS lead position and orientation. We validated the accuracy of the 7T imaging-based patient-specific model of the STN and m... Read more

The matrix protein M1 of the Influenza A virus is considered to mediate viral assembly and budding at the plasma membrane (PM) of infected cells. In order for a new viral particle to form, the PM lipid bilayer has to bend into a vesicle towards the extracellular side. Studies in cellular models have proposed that different viral proteins might be responsible for inducing membrane curvature in this context (including M1), but a clear consensus has not been reached. In this study, we use a comb... Read more

Lamellar bodies (LBs) are surfactant rich organelles in alveolar type 2 cells. LBs disassemble into a lipid-protein network that reduces surface tension and facilitates gas exchange at the air-water interface in the alveolar cavity. Current knowledge of LB architecture is predominantly based on electron microscopy studies using disruptive sample preparation methods. We established a post-correlation on-lamella cryo-correlative light and electron microscopy approach for cryo-FIB milled lung ce... Read more

Until March 2021, around 120 million coronavirus disease (COVID-19) infected cases and over 2.6 million deaths have been reported worldwide. […] Recent investigations have implied that face masks help to reduce the disease transmission and therefore slow down the growth of the epidemic curve. However, there are still ongoing debates on the efficacy of wearing masks […] since there is a general lack of information relating to the material structure of commonly used face masks.Read more

Unprecedented combination of resolution, field of view and contrast for the analysis human enamel carious lesions was achieved. Synchrotron X-ray micro-computed tomography revealed sub-micron details of enamel rod and inter-rod regions inaccessible by laboratory tomography. Successful segmentation and labelling allowed the extraction of enamel etching patterns and statistics. Correlation was obtained between synchrotron X-ray micro-tomography and FIB-SEM cross-sec... Read more

Decommissioning of the damaged Chernobyl nuclear reactor Unit 4 is a top priority for the global community. Before such operations begin, it is crucial to understand the behaviour of the hazardous materials formed during the accident. Since those materials formed under extreme and mostly unquantified conditions, modelling alone is insufficient to accurately predict their physical, chemical and, predominantly, mechanical behaviour. Meanwhile, knowledge of the mechanical characteristics of thos... 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

Many of the grand challenges in volcanic and magmatic research are focused on understanding the dynamics of highly heterogeneous systems and the critical conditions that enable magmas to move or eruptions to initiate. However, we are usually unable to observe the processes directly. Here we give a short synopsis of the new capabilities and highlight the potential insights that in situ observation can provide. We present the first 3D data showing the evolving textural heterogeneity within a sh... Read more

In order to provide the population with consistent and science-based advice on preferred materials for face masks, we are characterizing the microstructure of different materials using X-ray microfocus computed tomography (microCT), and we use these datasets to simulate the pressure drop (i.e. measure for breathability). We validate our measurements with physically measured filter efficiency and pressure drop, and in this way, we try to develop a “virtual testing platform” for the charac... Read more

In China’s energy consumption structure, coal is the main energy source, accounting for about 60% of primary energy consumption. Coal is a porous medium with complex pore structures. Nanopore structure in coal particle is the basic underlying factor driving coal particle strength. A better knowledge of nanopore structure – coal particle strength correlation is of great significance for coal mining and other fields of engineering problems.

The subtalar joint describes an articulation between talus and calcaneus, forming one of two joints of the hindfoot with the tibiotalar or ankle joint above the talus and the subtalar joint below. The talus comprises of three facets (anterior, middle and posterior) that articulate with the mating facets on the calcaneus at the subtalar joint. The bones are connected by a complex of ligamentous structures that connect the talus to the calcaneus and both structures to the adjacent navicular bon... 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

An elemental sulfur electrode was imaged with X-ray micro and nano computed tomography and segmented into its constituent phases. Morphological parameters including phase fractions and pore and particle size distributions were calculated directly from labelled image data, and flux based simulations were performed to determine the effective molecular diffusivity of the pore phase and electrical conductivity of the conductive carbon and binder phase, D... 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