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 endoplasmic reticulum (ER) extends throughout a cell and plays a critical role in maintaining cellular homeostasis.
Changes in ER shape could provide a clue to explore the mechanisms that underlie the fate determination of neurons after
axon injury because the ER drastically changes its morphology under neuronal stress to maintain cellular homeostasis and
recover from damage. Because of their tiny structures and richness in the soma, the detailed morphology of the ER and... Read more

Focused-ion beam-scanning electron microscopic (FIB-SEM) tomography enables easier acquisition of a series of ultrastructural, sectional images directly from resin-embedded biological samples. In this study, to clarify the three-dimensional (3D) architecture of glomerular endothelial cells (GEnCs) in adult rats, we manually extracted GEnCs from serial FIB-SEM images and reconstructed them on an Amira reconstruction software. The luminal and basal surface structures were clearly visualized in ... 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

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

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

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

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

Solid–liquid interfaces are important in a range of chemical, physical and biological processes but are often not fully understood owing to the lack of high-resolution characterization methods that are compatible with both solid and liquid components. For example, the related processes of dendritic deposition of lithium metal and the formation of solid–electrolyte interphase layers are known to be key determinants of battery safety and performance in high-energy-density lithium-metal bat... Read more

4D imaging – the three-dimensional distributions of chemical species determined using multi-energy X-ray tomography – of cathode catalyst layers of polymer electrolyte membrane fuel cells (PEM-FC) has been measured by scanning transmission x-ray microscopy (STXM) spectro-tomography at the C 1s and F 1s edges. In order to monitor the effects of radiation damage on the composition and 3D structure of the perfluorosulfonic acid (PFSA) ionomer, the same volume was measu... Read more

The appearance of wings in insects, early in their evolution [1], has been one of the more critical innovations contributing to their extraordinary diversity. Despite the conspicuousness and importance of wings, the origin of these structures has been difficult to resolve and represented one of the “abominable mysteries” in evolutionary biology [2]. More than a century of debate has boiled the matter down to two competing alternatives—one of wings representing an extension of the thorac... 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

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

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

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

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