Welcome to the Amira-Avizo Software Use Case Gallery

Recycling spent lithium-ion batteries (LiBs) guarantees the conservation of important metal resources by reducing demands on raw supply and offsetting the energy and environmental costs associated with its manufacture. Employing a molten salt as a solvent for extraction affords a much greener and simpler route to metal recovery by electrochemical means. The current mechanistic understanding of the electrochemical recovery of metals in molten salts needs to be improved for the process to be op... Read more

Despite advances in imaging, image-based vascular systems biology has remained challenging because blood vessel data are often available only from a single modality or at a given spatial scale, and cross-modality data are difficult to integrate.

Therefore, there is an exigent need for a multimodality pipeline that enables ex vivo vascular imaging with magnetic resonance imaging, computed tomography and optical microscopy of the same sample, while permitting imaging with complementary c... Read more

During the last decades, X-ray (micro-)computed tomography has gained increasing attention for the description of porous skeletal and shell structures of various organism groups. However, their quantitative analysis is often hampered by the difficulty to discriminate cavities and pores within the object from the surrounding region. Herein, we test the ambient occlusion (AO) algorithm and newly implemented optimisations for the segmentation of cavities (implemented in the software Amira). (... 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

For organic-inorganic composite materials, the spatial dispersion of inorganic fillers in the organic matrix is of great significance for designing and manufacturing high-performance composite materials. To improve the understanding of the micro-physical mechanism of the filler-reinforced polymer matrix, we studied the relationship between filler network structure and macro-mechanical properties of silicone rubber by using fluorescent labeling technology and three-dimensional (3D) visualizati... Read more

The prevailing electrode fabrication method for lithium-ion battery electrodes includes calendering at high pressures to densify the electrode and promote adhesion to the metal current collector.

However, this process increases the tortuosity of the pore network in the primary transport direction and imposes severe tradeoffs between electrode thickness and rate capability. With the aim of understanding the impact of pore tortuosity on electrode kinetics, and enabling cell designs with ... Read more

Cortical bone is permeated by a system of pores, occupied by the blood supply and osteocytes. With ageing, bone mass reduction and disruption of the microstructure are associated with reduced vascular supply. Insight into the regulation of the blood supply to the bone could enhance the understanding of bone strength determinants and fracture healing. Using synchrotron radiation-based computed tomography, the distribution of vascular canals and osteocyte lacunae was assessed in murine cortica... Read more

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

To accurately predict the initiation and evolution of uranium hydride potentially present in nuclear waste containers, studies of simulated conditions are required.

Here, for the first time, the uranium-deuterium reaction was examined in-situ, in real time, whilst within grouted media. A deuterium gas control rig and stainless steelquartz glass reaction cell were configured on a synchrotron beam line to collect X-ray diffraction and X-ray tomography data. It was found that deuteride fo... Read more

Evidence for macroscopic life in the Paleoproterozoic Era comes from 1.8 billion-year-old (Ga) compression fossils [Han TM, Runnegar B (1992) Science 257:232–235; Knoll et al. (2006) Philos Trans R Soc Lond B 361:1023–1038],  Stirling biota [Bengtson S et al. (2007) Paleobiology 33:351–381], and large colonial organisms exhibiting signs of coordinated growth from the 2.1-Ga Francevillian series, Gabon. Here we report on pyritized string-shaped structures from... Read more

Microscopic organisms that penetrate calcareous structures by actively dissolving the carbonate matrix, namely microendoliths, have an important influence on the breakdown of marine carbonates.

Microscopic organisms that penetrate calcareous structures by actively dissolving the carbonate matrix, namely microendoliths, have an important influence on the breakdown of marine carbonates. The study of these microorganisms and the bioerosion traces they produce is crucial for understanding ... Read more

Malignant cells are surrounded by a complex and supportive tumor microenvironment that consists of immune cells, extracellular matrix, vasculature, and fibroblasts. Cancer-associated fibroblasts (CAF) are the major cell type in the reactive stroma and are known to promote tumorigenesis and metastasis. Fibroblast activation protein alpha (FAP) is a transmembrane serine protease expressed by CAFs in the microenvironment of epithelial tumors.

Meta-analysis of FAP expression and clinical ... 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

A shift in environmental conditions impacts the evolution of complex developmental and behavioral traits. The Mexican cavefish, Astyanax mexicanus, is a powerful model for examining the evolution of development, physiology, and behavior because multiple cavefish populations can be compared to an extant and ancestral-like surface population of the same species. Many behaviors have diverged in cave populations of A. mexicanus, and previous studies have shown that cavefish ha... Read more

Neurons project axons to local and distal sites and can display heterogeneous morphologies with limited physical dimensions that may influence the structure of large organelles such as mitochondria. Using cryo-electron tomography (cryo-ET), we characterized native environments within axons and presynaptic varicosities to examine whether spatial restrictions within these compartments influence the morphology of mitochondria. Segmented tomographic reconstructions revealed distinctive morphologi... Read more

Shelled pteropods are widely regarded as bioindicators for ocean acidification, because their fragile aragonite shells are susceptible to increasing ocean acidity. While short-term incubations have demonstrated that pteropod calcification is negatively impacted by ocean acidification, we know little about net calcification in response to varying ocean conditions in natural populations. Here, we examine in situ calcification of Limacina helicina pteropods collected from the California... 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 recent years, due to the rapid development of industrial lightweight technology, composite materials based on fiber reinforced plastics (FRP) have been widely used in the industry. However, the environmental impact of the FRPs is higher each year. To overcome this impact, co-injection molding could be one of the good solutions. But how to make the suitable control on the skin/core ratio and how to manage the glass fiber orientation features are still significant challenges. In this study, ... Read more

The cracking process in Longmaxi formation shale was experimentally studied during uniaxial compressive loading. Both the evolution of the three-dimensional fracture network and the micromechanics of failure in the layered shale were examined as a function of the inclination angle of the bedding plane. To visualize the cracking process, the test devices presented here used an industrial X-ray CT scanner that enabled scanning during the uniaxial compressive loading. Scanning electron microscop... 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

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