Welcome to the Amira-Avizo Software Use Case Gallery

Immunofluorescence tomography is a high-resolution 3-D reconstruction method based on methacrylate embedding and serial-sectioning, where 2-D images of immuno-stained serial-sections are computationally aligned into image stacks, and the 3-D volume rendered. Butyl-Methyl Methacrylate (BMMA) plastic was adopted as it preserves excellent tissue morphology and can be de-plasticized easily using an organic solvent, which enables immuno-staining of serial-sections without antibody penetration issu... Read more

Protein aggregation and dysfunction of the ubiquitin-proteasome system are hallmarks of many neurodegenerative diseases. Here, we address the elusive link between these phenomena by employing cryo-electron tomography to dissect the molecular architecture of protein aggregates within intact neurons at high resolution. We focus on the poly-Gly-Ala (poly-GA) aggregates resulting from aberrant translation of an expanded GGGGCC repeat in C9orf72, the most common genetic cause of amyotrophic latera... Read more

COPI-coated vesicles mediate trafficking within the Golgi apparatus and from the Golgi to the endoplasmic reticulum. Here, we applied cryo-focused ion beam milling, cryo-electron tomography and subtomogram averaging to determine the native structure of the COPI coat within vitrified Chlamydomonas reinhardtii cells. The native algal structure resembles the in vitro mammalian structure, but additionally reveals cargo bound beneath beta’–COP. We find that all coat components disassemble... Read more

Microorganisms are the chief primary producers within present-day deep-sea hydrothermal vent ecosystems, and play a fundamental role in shaping the ecology of these environments. (…) The oldest known hydrothermal vent community that includes metazoans is preserved within the Ordovician to early Silurian Yaman Kasy massive sulfide deposit, Ural Mountains, Russia. (…) A re-examination of these fossils using a range of microscopy, chemical analysis and nano-tomography techniques re... Read more

A new genus and species of colubroid snake is described from the isolated highlands of western Chiapas. This enigmatic little snake possesses a unique suite of characters that defies placing it in any known genus and clearly distinguishes it from all known genera. Several of the most unusual features include subcaudals undivided throughout the length of the tail and a simple hemipenis completely adorned with calyces and having a sulcus spermaticus that remains unbifurcated until the apical po... Read more

The orchestration of intercellular communication is essential for multicellular organisms. One mechanism by which cells communicate is through long, actin-rich membranous protrusions called tunneling nanotubes (TNTs), which allow the intercellular transport of various cargoes, between the cytoplasm of distant cells in vitro and in vivo. Here, we use correlative FIB-SEM, light- and cryo-electron microscopy approaches to elucidate the structural organization of neuronal TNTs. Our data indicate ... Read more

Fossil fruits formerly described as cashews from the Oligocene of Peru are reinvestigated based on the original specimens and newly collected materials. The recovery of an outer spiny layer, preserved in the sedimentary molds surrounding the locule casts, indicates that these disseminules do not represent Anacardium. Imagery from nano-CT scans of the specimens documents a distinctive morphology which does not resemble any fruits or seeds of Anacardiaceae. We describe the morphology in more de... Read more

The hot pressing process for fabricating membrane electrode assemblies (MEAs) has been widely adopted, yet little is known of its effects on the microstructural properties of the different components of the MEA. In particular, the interaction of the electrolyte, electrode and gas diffusion layer (GDL) due to lamination is difficult to probe as conventional imaging techniques cannot access the internal structure of the MEA. Here, a novel approach is used, which combines characterisation of hot... Read more

The paper proposes a new experimental methodology, based on ultrasonic measurements, that aims at evaluating the anisotropic damage in woven semi-crystalline polymer composites through new damage indicators. Due to their microstructure, woven composite materials are characterized by an anisotropic evolution of damage induced by different damage mechanisms occurring at the micro or mesoscopic scales. In this work, these damage modes in polyamide 6.6/6-woven glass fiber reinforced composites ha... Read more

The vanadium redox flow battery (VRFB) has emerged as a promising technology for large-scale storage of intermittent power generated from renewable energy sources due to its advantages such as scalability, high energy efficiency and low cost. In the current study, a three-dimensional(3D) Lattice Boltzmann model is developed to simulate the transport mechanisms of electrolyte flow, species and charge in the vanadium redox flow battery at the micro pore scale. An electrochemical model using the... Read more

The interest in potential applications produced with self-compacting fibre reinforced concrete continues to grow, but in practice, problems associated with an uneven distribution and orientation of fibres in the concrete structure occur. It is not clear what exactly influences uneven distribution of fibres in selfcompacting concrete (SCC) mixtures, especially during the casting and how different factors influence fibre orientation. The objective of this work was to investigate how rheological... Read more

In this paper a study concerning an automatic determination of distribution of steel fibres in self-compacting concrete (SCC) is presented. The determination of fibre distribution is required to assess any relationship between those features and casting methods of concrete elements. Concrete beams with steel fibres of various types and casting methods were examined. Involved methods were computed tomography imaging followed by image analysis. After image analysis a label map consisting of all... Read more

It is shown that approximately 2wt% of graphene in the matrix of a unidirectionally-reinforced carbon fiber epoxy composite leads to a significant enhancement in mechanical properties. Particularly, it is found that the axial stiffness of the composites is increased by 10GPa accompanied by an increase in axial strength of 200MPa.

The fruit fly, Drosophila melanogaster, is an important experimental model to address central questions in neuroscience at an organismic level. However, imaging of neural circuits in intact fruit flies is limited due to structural properties of the cuticle. Here we present a novel approach combining tissue clearing, ultramicroscopy, and data analysis that enables the visualisation of neuronal networks with single-cell resolution from the larval stage up to the adult Drosophila. (…) This... Read more

The porous transport layer (PTL) is a vital component of the polymer electrolyte membrane water electrolyser (PEMWE) as it is both a conduit for current distribution and mass transport. This study aims to examine the influence of the microstructure of the PTL on the performance of a PEMWE by the combination of ex-situ and in-situ techniques. Two PTLs with distinctly different mean pore diameter were characterized to determine key properties such as surface morphology, porosity, pore size dist... Read more

The size and shape of the Neandertal thorax has been debated since the first discovery of Neandertal ribs more than 150 years ago, with workers proposing different interpretations ranging from a Neandertal thoracic morphology that is indistinguishable from modern humans, to one that was significantly different from them. Here, we provide a virtual 3D reconstruction of the thorax of the adult male Kebara 2 Neandertal. Our analyses reveal that the Kebara 2 thorax is significantly different but ... Read more

Wind-dispersed plants have evolved ingenious ways to lift their seeds. The common dandelion uses a bundle of drag-enhancing bristles (the pappus) that helps to keep their seeds aloft. This passive flight mechanism is highly effective, enabling seed dispersal over formidable distances; however, the physics underpinning pappus-mediated flight remains unresolved. Here we visualized the flow around dandelion seeds, uncovering an extraordinary type of vortex. This vortex is a ring of recirculating... Read more

Proinflammatory mononuclear phagocytes (MPs) play a crucial role in the progression of multiple sclerosis (MS) and other neurodegenerative diseases. Despite advances in neuroimaging, there are currently limited available methods enabling noninvasive detection of MPs in vivo. Interestingly, upon activation and subsequent differentiation toward a proinflammatory phenotype MPs undergo metabolic reprogramming that results in increased glycolysis and production of lactate. Hyperpolarized (HP) Read more

Salmonella Typhimurium (S.Tm) is an enteropathogen requiring multiple virulence factors, including two type three secretion systems (T1 and T2). T1 triggers epithelium invasion in which the bacteria are taken up into endosomes that mature into Salmonella-containing vacuoles (SCV) and trigger T2 induction upon acidification. Mechanisms controlling endosome membrane integrity or pathogen egress into the cytosol are incompletely understood. We screened for host factors affecting invasion and SCV... Read more

Neuromuscular junction degeneration is a prominent aspect of sarcopenia, the age-associated loss of skeletal muscle integrity. Previously, we showed that muscle stem cells activate and contribute to mouse neuromuscular junction regeneration in response to denervation (Liu et al., 2015). Here, we examined gene expression profiles and neuromuscular junction integrity in aged mouse muscles, and unexpectedly found limited denervation despite a high level of degenerated neuromuscular junctions. In... Read more

Here we report the oldest fossil skeleton of a flying squirrel (11.6 Ma) that displays the gliding-related diagnostic features shared by extant forms and allows for a recalibration of the divergence time between tree and flying squirrels. Our phylogenetic analyses combining morphological and molecular data generally support older dates than previous molecular estimates (~23 Ma), being congruent with the inclusion of some of the earliest fossils (~36 Ma) into this clade. They also show that fl... Read more