Welcome to the Amira-Avizo Software Use Case Gallery

Positive-strand RNA viruses, which can be devastating pathogens in humans, animals and plants, replicate their genomes on intracellular membranes. Here, we describe the three-dimensional ultrastructural organization of a tombusvirus replicase in yeast, a valuable model for exploring virus–host interactions…

Intravital microscopy provides dynamic understanding of multiple cell biological processes, but its limited resolution has so far precluded structural analysis. Because it is difficult to capture rare and transient events, only a few attempts have been made to observe specific developmental and pathological processes in animal models using electron microscopy. The multimodal correlative approach that we propose here combines intravital microscopy, microscopic X-ray computed tomography and thr... Read more

HIV-1 maturation occurs via multiple proteolytic cleavages of the Gag polyprotein, causing rearrangement of the virus particle required for infectivity. (…) How individual cleavages contribute to changes in protein structure and interactions, and how the mature, conical capsid forms, are poorly understood. Here, we employed cryoelectron tomography to determine morphology and high-resolution CA lattice structures for HIV1 derivatives in which Gag cleavage sites are mutated. These analyse... Read more

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

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

Analysis of neuronal arborization and connections is a powerful tool in fundamental and clinical neuroscience. Changes in neuronal morphology are central to brain development and plasticity and are associated with numerous diseases. Golgi staining is a classical technique based on a deposition of metal precipitate in a random set of neurons. Despite their versatility, Golgi methods have limitations that largely precluded their use in advanced microscopy. We combined Golgi staining with fluore... Read more

Podocytes present a unique 3D architecture specialized for glomerular filtration. However, several 3D morphological aspects on podocyte development remain partially understood because they are difficult to reveal using conventional scanning electron microscopy (SEM). Here, we adopted serial block-face SEM imaging…

In biomedical research, a huge variety of different techniques is currently available for the structural examination of small specimens, including conventional light microscopy (LM), transmission electron microscopy (TEM), confocal laser scanning microscopy (CLSM), microscopic X-ray computed tomography (microCT), and many others. Since every imaging method is physically limited by certain parameters, a correlative use of complementary methods often yields a significant broader range of inform... Read more

Correlative light and electron microscopy (CLEM) is a powerful approach to investigate the molecular ultrastructure of labeled cell compartments. However, quantitative CLEM studies are rare, mainly due to small sample sizes and the sensitivity of fluorescent proteins to strong fixatives and contrasting reagents for EM. Here, we show that fusion of…

Serial block-face electron microscopy (SBEM) provides nanoscale 3D ultrastructure of embedded and stained cells and tissues in volumes of up to 10⁷ µm³. In SBEM, electrons with 1–3 keV energies are incident on a specimen block, from which backscattered electron (BSE) images are collected with x, y resolution of 5–10 nm in the block-face plane, and successive layers are removed by an in situ ultramicrotome. Sp... 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

It is well known that the phonatory process changes during the life span. However, detailed investigations on potential factors concerned are rare. To deal with this issue, we performed extended biomechanical, macro anatomical, and histological analyses of the contributing laryngeal structures in ex vivo juvenile sheep models. Altogether twelve juvenile sheep larynges were analyzed within the phonatory experiments. Three different elongation levels and 16 different flow levels were applied to... Read more

During the acts of biting and chewing, the muscles of the jaw (consisting of the masseter, temporalis, and medial pterygoid in the elevator group, and lateral pterygoid as the main depressor) generate forces that dictate jaw kinematics . The movement of jaws hinges about the temporomandibular joint and are brought together by the muscles attached to respective bones through bone-tendon interfaces known as entheses . Thus, chewing forces affect aspects of craniofacial structure as well as bo... Read more

At GEVES, Microtomography (micro-CT), which is a technique using X-rays to investigate internal anatomy and morphology of organisms without destruction, is applied to plant seed quality control and phenotyping. Several applications have been developed using micro-CT coupled with Avizo software development, such as for example in the Measurements of internal and external sugar beet seed structures for seed phenotyping

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

External and internal morphological characters of extant and fossil organisms are crucial to establishing their systematic position, ecological role and evolutionary trends. (…) We found well-preserved three-dimensional anatomy in mineralized arthropods from Paleogene fissure fillings and demonstrate the value of these fossils by utilizing digitally reconstructed anatomical structure of a hister beetle. The new anatomical data facilitate a refinement of the species diagnosis and allowed... 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

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 aim of this study was to see the effect of Er:YAG laser irradiation in dentine and compare this with its effect in enamel. The mechanism of crack propagation in dentine was emphasised and its clinical implications were discussed. A possible mechanism is that laser radiation is transmitted down the dentinal tubules causing micro-cracks to form in the dentinal tubule walls that tend to be limited to this region. Crack might be a source of fracture as it represents a weak point and subsequen... Read more

Sediment plates (a type of lacquer peels) represent a sampling method whereby a thin plate of undisturbed sediments is obtained directly from the outcrop. A low-viscosity, hardening epoxy resin is applied to a freshly exposed cross-section of an unconsolidated deposit and impregnates a surface layer of the cross-section via capillary forces before solidifying. Upon hardening, a solid plate (0.5–5 cm thick and up to 2 m in length) of the sedimentary formation can be recovered and transported... Read more