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

Pigment distributions have a critical role in the corrosion protection properties of organic paint coatings, but they are difficult to image in 3D over statistically significant volumes and at sufficiently high spatial resolutions required for detailed analysis. Here we report, for the first time, large volume analytical serial sectioning tomography of an organic composite coating using a xenon Plasma Focused Ion Beam (PFIB) combined with secondary electron imaging, energy dispersive X-ray (E... Read more

Reprocessing of spent nuclear fuels using molten salt media is an attractive alternative to liquid-liquid extraction techniques.

Pyroelectrochemical processing utilizes direct, selective, electrochemical reduction of uranium dioxide, followed by selective electroplating of a uranium metal. Thermodynamic prediction of the electrochemical reduction of UO2 to U in LiCl-KCl eutectic has shown to be a function of the oxide ion activity. The pO2 of the salt may be affected by the microstruc... Read more

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

Unlike white and brown adipose tissues, the bone marrow adipocyte (BMA) exists in a microenvironment containing unique populations of hematopoietic and skeletal cells.

To study this microenvironment at the subcellular level, we performed a three-dimensional analysis of the ultrastructure of the BMA niche with focused ion beam scanning electron microscopy (FIB-SEM). This revealed that BMAs display hallmarks of metabolically active cells including polarized lipid deposits, a dense mitoch... Read more

Recent studies have identified gold nanoparticles in ores in a range of deposit types, but little is known about their formation processes. In this contribution, gold-bearing magnetite from the well-documented, world-class Beiya Au deposit, China, was investigated in terms of microstructure and crystallography at the nanoscale. We present the first three-dimensional (3D) focused ion beam/scanning electron microscopy (FIB/SEM) tomography of the distribution of gold nanoparticles in nanopores i... Read more

A combination of 3D tomography techniques provides direct evidence that links the phase assemblage to the bio-corrosion behaviour of a magnesium-zinc-calcium (Mg-Zn-Ca) alloy. The true shape, connectivity and volume fraction of the components have been determined using focused ion beam (FIB) tomography. The mechanism of the effect of the components with different morphologies on biodegradation was studied with the help of FIB. Micro X-ray CT (MicroCT) was used to investigate the degradation o... Read more

Nickel-yttria-stabilized zirconia (Ni-YSZ) cermet is widely used as an anode material in solid oxide fuel cells (SOFCs); however, Ni re-oxidation causes critical problems due to volume expansion, which causes high thermal stress. We fabricated a Ni-YSZ anode functional layer (AFL), which is an essential component in high-performance SOFCs, and re-oxidized it to investigate the related three-dimensional (3D) microstructural and thermo-mechanical effects. A 3D model of the re-oxidized AFL ... Read more

Growing popularity and rapid development of Solid Oxide Fuel Cells (SOFCs) stem for their potential to become a gamechanger in the field of clean power generation technologies.

In this paper, a transient microstructure-oriented numerical simulation of a planar Direct Internal Reforming Solid Oxide Fuel Cell (DIR-SOFC) is delivered. The performance criteria in a direct steam reforming for a fuel starvation scenario are analyzed in order to optimize the underlying process. The proposed t... Read more

The performance of electrochemical devices depends on the three-dimensional (3D) distributions of microstructural features in their electrodes. Several mature methods exist to characterize 3D microstructures over the microscale (tens of microns), which are useful in understanding homogeneous electrodes. However, methods that capture mesoscale (hundreds of microns) volumes at appropriate resolution (tens of nm) are lacking, though they are needed to understand more common, less ideal electrode... 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

While fluorescence microscopy provides tools for highly specific labeling and sensitive detection, its resolution limit and lack of general contrast has hindered studies of cellular structure and protein localization. Recent advances in correlative light and electron microscopy (CLEM), including the fully integrated CLEM workflow instrument, the Thermo Scientific CorrSight with MAPS, have allowed for a more reliable, reproducible, and quicker approach to correlate three-dimensional time-lapse... Read more

High-resolution 3D images of organelles are of paramount importance in cellular biology. Although light microscopy and transmission electron microscopy (TEM) have provided the standard for imaging cellular structures, they cannot provide 3D images.

However, recent technological advances such as serial block-face scanning electron microscopy (SBF-SEM) and focused ion beam scanning electron microscopy (FIB-SEM) provide the tools to create 3D images for the ultrastructural analysis of org... Read more

Cells contain hundreds of different organelle and macromolecular assemblies intricately organized relative to each other to meet any cellular demands. Obtaining a complete understanding of their organization is challenging and requires nanometer-level, three-dimensional reconstruction of whole cells. Even then, the immense size of datasets and large number of structures to be characterized requires generalizable, automatic methods.

To meet this challenge, we developed an analy... Read more

Enamel caries is a highly prevalent worldwide disease that involves the demineralisation of the outer tooth structure. In this study, we report the analysis of artificially demineralised human enamel sections (‘slices’) etched using lactic acid (2% v/v) in comparison with healthy enamel using correlative techniques of optical and electron microscopy, as well as scanning diffraction. Demineralisation of the enamel was characterised at the micron to sub-micron scale. The structure of the he... 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

High market demands related to material quality and properties strongly influence redesigning of common safety loaded aluminum alloy castings. The quality of aluminum components and associated obtained mechanical properties are strongly dependent on the casting process and parameters, as well as on the chemical composition. Therefore, the redesigning of chemical composition of high-strength aluminum alloys becomes significant for safety critical structural components in automotive industry.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

Coated paper is an example of a multi-layer porous medium, involving a coating layer along the two surfaces of the paper and a fibrous layer in the interior of the paper. The interface between these two media needs to be characterized in order to develop relevant modeling tools. After careful cutting of the paper, a cross section was imaged using focused ion beam scanning electron microscopy. The resulting image was analyzed to characterize the coating layer and its transition to the fibrous ... Read more

The development of focused ion beam-scanning electron microscopy (FIB-SEM) techniques has allowed high-resolution 3D imaging of nanometre-scale porous materials. These systems are of important interest to the oil and gas sector, as well as for the safe long-term storage of carbon and nuclear waste. This work focuses on validating the accurate representation of sample pore space in FIB-SEM-reconstructed volumes and the predicted permeability of these systems from subsequent single-phase flow s... Read more

This study presents a technique to directly characterize the carbon and binder domain (CBD) in lithium-ion (Li-ion) battery electrodes in three dimensions and use it to determine the effective transport properties of a LiNi_0.33Mn_0.33Co_0.33O₂ (NMC) electrode. X-ray nanocomputed tomography (nano-CT) is used to image an electrode composed solely of carbon and binder, whereas focused ion beam–scanning electron microscopy is used to analyze cross-sect... Read more