Welcome to the Amira-Avizo Software Use Case Gallery

Mammalian epididymal epithelial cells are crucial for sperm maturation. Historically,
vacuole-like ultrastructures in epididymal epithelial cells were
observed via transmission electron microscopy but were undefined. Here, we
utilize volume electron microscopy (vEM) to generate 3D reconstructions of
epididymal epithelial cells and identify these vacuoles as intercellular organelle
reservoirs (IORs) in the lateral intercellular space (LIS), which contains
pr... Read more

Many physiological, biomechanical, evolutionary and clinical studies that explore skeletal structure and function require successful separation of trabecular from cortical compartments of a bone that has been imaged by X-ray micro-computed tomography (micro-CT) prior to analysis. Separation often involves manual subdivision of these two similarly radio-opaque compartments, which can be time-consuming and subjective. We have developed an objective, semi-automated protocol which reduces user bi... Read more

Computed tomography (CT) enables rapid imaging of large-scale studies of bone, but those datasets typically require manual segmentation, which is time-consuming and prone to error. Convolutional neural networks (CNNs) offer an automated solution, achieving superior performance on image data. In this methodology-focused paper, we used CNNs to train segmentation models from scratch on 2D and 3D patches from micro-CT scans of otter long bones. These new models, collectively called BONe (Bone One... Read more

Alphaviruses are mosquito-borne viruses that cause serious disease in humans and other mammals. Along with its mosquito vector, the Alphavirus chikungunya virus (CHIKV) has spread explosively in the last 20 years, and there is no approved treatment for chikungunya fever. On the plasma membrane of the infected cell, CHIKV generates dedicated organelles for viral RNA replication, so-called spherules. Whereas structures exist for several viral proteins that make up the spherule, ... Read more

The liver contains a variety of vessels and participates in miscellaneous physiological functions. While past studies generally focused on certain hepatic vessels, we simultaneously obtained all the vessels and cytoarchitectural information of the intact mouse liver lobe at single-cell resolution. […] providing a technology roadmap for studying the fine hepatic vascular structures and their spatial relationship, which will help research into liver diseases and evaluation of medical effi... Read more

Ebola viruses (EBOVs) assemble into filamentous virions, whose shape and stability are determined by the matrix viral protein 40 (VP40). Virus entry into host cells occurs via membrane fusion in late endosomes; however, the mechanism of how the remarkably long virions undergo uncoating, including virion disassembly and nucleocapsid release into the cytosol, remains unknown. Here, we investigate the structural architecture of EBOVs entering host cells and discover that the VP40 matrix disassem... 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

3D characterisation of the particle kinematics during loess collapse is performed based on X-ray micro-computed tomography.

Particle displacements and rotations associated with the collapse are determined.

The volumetric strain is shown to be significantly heterogeneous at single-particle scale.

The evolution of particle-to-particle contacts is found to be much more complex than previously stated.

An apparatus is specially designed to perf... 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

Our team is developing a modern, cross-disciplinary approach to documentation and preservation of astromaterials, specifically lunar and meteorite samples stored at the Johnson Space Center (JSC) Lunar Sample Laboratory Facility.

Apollo Lunar Sample 60639, collected as part of rake sample 60610 during the 3rd Extra-Vehicular Activity of the Apollo 16 mission in 1972, served as the first NASA preserved lunar sample to be examined by our team in the development of a novel approach to int... 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

TRISO particles, a composite nuclear fuel built up by ceramic and graphitic layers, have outstanding high temperature resistance. TRISO fuel is the key technology for High Temperature Reactors (HTRs) and the Generation IV Very High Temperature Reactor (VHTR) variant.

TRISO offers unparalleled containment of fission products and is extremely robust during accident conditions. An understanding of the thermal performance and mechanical properties of TRISO fuel requires a detailed knowledg... 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

Amira capacities for membranes and filaments segmentation in cryo-TEM images are featured on the front cover of Biochemical Journal, July 2020.

Budding yeast septins are essential for cell division and polarity. (…) [The authors] have dissected, here, for the first time, the behavior of the Shs1 protomer bound to membranes at nanometer resolution, in complex with the other septins. Using electron microscopy, [the authors] have shown that on membranes, Shs1 protomers self-assembl... 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

The Braconidae are a megadiverse and ecologically highly important group of insects. The vast majority of braconid wasps are parasitoids of other insects, usually attacking the egg or larval stages of their hosts. The ovipositor plays a crucial role in the assessment of the potential host and precise egg laying. We used lightand electron-microscopic techniques to investigate all inherent cuticular elements of the ovipositor (the female 9th abdominal tergum, two pairs of valvifers, and three p... Read more

Micro-computed tomography (μCT) is a valuable imaging modality for longitudinal quantification of bone volumes to identify disease or treatment effects for a broad range of conditions that affect bone health. Complex structures, such as the hindpaw with up to 31 distinct bones in mice, have considerable analytic potential, but quantification is often limited to a single bone volume metric due to the intensive effort of manual segmentation. Herein, we introduce a high-throughput, user-friendl... 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

Nickel-rich transition metal oxide materials […] are of great interest for achieving immediate improvements in the energy density of Li-ion batteries and for risk reduction within the Li-ion battery supply chain.
[…] An increase in Ni content in NMC materials leads to accelerated degradation […]. This potentially complicates their adoption in applications requiring extended cycle life such as in electric vehicles.

Recent developments in X-ray characterization to... Read more