Welcome to the Amira-Avizo Software Use Case Gallery

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

Actin waves are dynamic supramolecular structures involved in cell migration, cytokinesis, adhesion, and neurogenesis. Although wave-like propagation of actin networks is a widespread phenomenon, the actin architecture underlying wave propagation remained unknown. In situ cryo-electron tomography of Dictyostelium cells unveils the wave architecture and provides evidence for wave progression by de novo actin nucleation. Subtomogram averaging reveals the structu... 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

A novel archaeal virus, denoted Sulfolobus ellipsoid virus 1 (SEV1), was isolated from an acidic hot spring in Costa Rica. The morphologically unique virion of SEV1 contains a protein capsid with 16 regularly spaced striations and an 11-nm-thick envelope. The capsid exhibits an unusual architecture in which the viral DNA, probably in the form of a nucleoprotein filament, wraps around the longitudinal axis of the virion in... 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

The major mammalian bloodstream form of the African sleeping sickness parasite Trypanosoma bruceimultiplies rapidly, and it is important to understand how these cells divide. Organelle inheritance involves complex spatiotemporal re-arrangements to ensure correct distribution to daughter cells…

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

The Faroe Islands are a group of islands in the North Atlantic that are known for its natural beauty, Viking culture and a special population of house mouse. The Faroese house mouse from the most remote island of the Faroese, Mykines (population: 10 people), looked so distinct when it was discovered that it was declared a subspecies, Mus musculus faeroenesis. These mice are large-bodied and showed an extreme form of left-right asymmetry in its skull. Our research group has... Read more

Electrospun constructs for the repair of load-bearing tissues are required to have adequate mechanical properties. However, the failure mechanisms of electrospun fibrous materials are not well understood. Existing literature focuses on failure modes of individual fibers and/or on bulk mechanical properties of whole fiber mats.

Electrospinning allows the production of fibrous networks for tissue engineering, drug delivery, and wound healing in health care. It enables the production of c... Read more

Royal DSM is a global science-based company active in health, nutrition and
materials. Within DSM’s Materials Cluster DSM Engineering Plastics is a global player in specialty plastics. These materials are used in components for the electrical and electronics, automotive, flexible food packaging and consumer goods industries.

A typical product made of DSM Engineering Plastics’ polymer portfolio are USB-C connectors. Key performance indicators for this application are dimension... Read more

A team led by London Centre for Nanotechnology researchers, Prof. Ian Robinson and Dr. Bo Chen (now a professor at the Tongji University, Shanghai) used newly-developed serial block-face scanning electron microscopy (SBFSEM) and Thermo Scientific™ Avizo® Software, one dominant tool in 3D reconstructed image processing, to reveal the spatial structure of human chromosomes and nucleus quantitatively at high resolution of approximately 50 nm in three dimensions.