Welcome to the Amira-Avizo Software Use Case Gallery
Below you will find a collection of use cases of our 3D data visualization and analysis software. These use cases include scientific publications, articles, papers, posters, presentations or even videos that show how Amira-Avizo Software is used to address various scientific and industrial research topics.
Use the Domain selector to filter by main application area, and use the Search box to enter keywords related to specific topics you are interested in.
A unique approach to correlating an evolving 3D microstructure in an Al-Cu alloyand its micro-scale mechanical properties has been introduced. Using these nanoscale three-dimensional microstructures derived from Transmission X-rayMicroscopy (TXM), individual contributions from different strengthening mechanisms were quantified. The spatial distribution and morphology of the individual θ′ and θ phases were seen to play an important role in influencing dislocation storage. Uniaxi... Read more
C. Shashank Kaira, Christopher Kantzos, Jason J. Williams, Vincent De Andrade, Francesco De Carlo, Nikhilesh Chawlaa
Mesoscale characterization of local property distributions in heterogeneous electrodes
The performance of electrochemical devices depends on the three-dimensional (3D) distributions of microstructural features in their electrodes. Several mature methods exist to characterize 3D microstructures over the microscale (tens of microns), which are useful in understanding homogeneous electrodes. However, methods that capture mesoscale (hundreds of microns) volumes at appropriate resolution (tens of nm) are lacking, though they are needed to understand more common, less ideal electrode... Read more
Tim Hsu, William K. Epting, Rubayyat Mahbub, Noel T. Nuhfer, Sudip Bhattachary, Yinkai Lei, Herbert M. Miller, Paul R. Ohodnicki, Kirk R. Gerdes, Harry W. Abernathy, Gregory A. Hackett, Anthony D. Rollett, Marc De Graef, Shawn Litster, Paul A. Salvador
The three-dimensional (3D) characterization of nuclear fuel with X-ray microscopy has historically proven difficult, due to uranium’s high attenuation of easily accessible X-rays, both in a laboratory setting and at a synchrotron user facility. However, this imaging modality provides nondestructive information that can be used to investigate morphological changes arising from external stimuli (e.g., neutron irradiation, high-temperature testing).
Using an appropriate X-ray energy spe... Read more
Nikolaus L. Cordes, William C. Chuirazzi & Joshua J. Kane - John D. Stempien
A multi-scale approach for fracture simulation, based on the Cellular Automata technique, has been developed and then applied to a nuclear graphite that is used in structural components of the UK Advanced Gas-cooled Reactors (AGR).
High resolution X-ray computed tomographs of Gilsocarbon grade
graphite, with up to 68% weight loss by radiolytic oxidation, provide quantitative descriptions of the porosity within its constitutive filler particles and their surrounding matrix. The st... Read more
Yelena Vertyagina, Thomas James Marrow
Microstructural analysis of TRISO particles using multi-scale X-ray computed tomography
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
T. Lowe, R.S. Bradley, S. Yue, K. Barii, J. Gelb, N. Rohbeck, J. Turner, P.J. Withers
Masseter muscle function influences mandibular bone homeostasis. As previously reported, bone resorption markers increased in the mouse mandibular condyle two days after masseter paralysis induced with botulinum toxin type A (BoNTA), followed by local bone loss.
This study aimed to evaluate the bone quality of both the mandibular condyle and alveolar process in the mandible of adult mice during the early stage of a BoNTA‐induced masseter muscle atrophy, using a combined 3D histomorpho... Read more
Julián Balanta‐Melo, María Angélica Torres‐Quintana, Maximilian Bemmann, Carolina Vega, Constanza González, Kornelius Kupczik, Viviana Toro‐Ibacache, Sonja Buvinic
Synergistic role of nucleotides and lipids for the self-assembly of Shs1 septin oligomers
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
Cyntia Taveneau, Rémi Blanc, Gerard Pehau-Arnaudet, Aurélie Cicco, Aurélie Bertin
Ovipositor of the braconid wasp Habrobracon hebetor: structural and functional aspects
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
Michael Csader, Karin Mayer, Oliver Betz, Stefan Fischer, Benjamin Eggs
Protocols for Generating Surfaces and Measuring 3D Organelle Morphology Using Amira
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
Edgar Garza-Lopez, Zer Vue, Prasanna Katti, Kit Neikirk, Michelle Biete, Jacob Lam, Heather K. Beasley, Andrea G. Marshall, Taylor A. Rodman, Trace A. Christensen, Jeffrey L. Salisbury, Larry Vang, Margaret Mungai, Salma Ash Shareef, Sandra A. Murray, Jianqiang Shao, Jennifer Streeter, Brian Glancy, Renata O. Pereira1, E. Dale Abel, and Antentor Hinton, Jr.
The molecular basis for sarcomere organization in vertebrate skeletal muscle
Sarcomeres are force-generating and load-bearing devices of muscles. A precise molecular picture of how sarcomeres are built underpins understanding their role in health and disease. Here, we determine the molecular architecture of native vertebrate skeletal sarcomeres by electron cryo-tomography.
Our reconstruction reveals molecular details of the three-dimensional organization and interaction of actin and myosin in the A-band, I-band, and Z-disc and demonstrates that α-actinin cros... Read more
Zhexin Wang, Michael Grange, Thorsten Wagner, Ay Lin Kho, Mathias Gautel, Stefan Raunser
Osteocytes are the most frequent bone cells connected with each other through cell processes within tiny tubular-shaped canaliculi. The so-called osteocyte lacunar-canalicular network (LCN) plays a crucial role in bone remodeling and mineral homeostasis. Given the critical nature of these functions, it is herein hypothesized that the LCN must be structurally “overengineered” to provide network resilience.
This hypothesis is tested by characterizing canalicular networks in human bon... Read more
Emely Bortel, Liam M Grover, Neil Eisenstein, Christian Seim, Heikki Suhonen, Alexandra Pacureanu, Peter Westenberger, Kay Raum, Max Langer, Francoise Peyrin, Owen Addison, Bernhard Hesse
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
ChunTan, Andrew S.Leach, Thomas M.M. Heenan, Huw Parks, Rhodri Jervis, Johanna Nelson Weker, Daniel J.L. Brett, Paul R.Shearing
Collagen-Based Matrices for Osteoconduction: A Preclinical In Vivo Study
The aim of this study was to evaluate the influence of additional hydroxyapatite (HA) in collagen-based matrices (CM) and membrane placement on bone formation in calvarial defects.
Critical size defects in the calvaria of 16 New Zealand White Rabbits were randomly treated with CM or mineralized collagen-based matrices (mCM). Half of the sites were covered with a collagen membrane. Animals were euthanized after 12 weeks of healing. The samples were studied by micro-CT and histology. New... Read more
Hiroki Katagiri, Yacine El Tawil, Niklaus P. Lang, Jean-Claude Imber, Anton Sculean, Masako Fujioka-Kobayashi and Nikola Saulacic
Membrane architecture of pulmonary lamellar bodies revealed by post-correlation on-lamella cryo-CLEM
Lamellar bodies (LBs) are surfactant rich organelles in alveolar type 2 cells. LBs disassemble into a lipid-protein network that reduces surface tension and facilitates gas exchange at the air-water interface in the alveolar cavity. Current knowledge of LB architecture is predominantly based on electron microscopy studies using disruptive sample preparation methods. We established a post-correlation on-lamella cryo-correlative light and electron microscopy approach for cryo-FIB milled lung ce... Read more
Steffen Klein, Benedikt H. Wimmer, Sophie L. Winter, Androniki Kolovou, Vibor Laketa, Petr Chlanda
3D Dissection of Structural Membrane-Wall Contacts in Filamentous Moss Protonemata
Cell-to-cell contact is essential for communication and development of multicellular organisms. A prerequisite is the passage through membranes. That way, molecular exchange and information flow is regulated via hormones, membrane proteins and pores.
In plants, the rigid cell walls prevent large membrane contact areas between protoplasts. Only plasmodesmata, minute channels between adjacent cells, form direct connections. Often, molecular data of the proteins involved are manifold but t... Read more
Dominik Harant and Ingeborg Lang
The Architecture of Traveling Actin Waves Revealed by Cryo-Electron Tomography
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
Marion Jasnin, Florian Beck, Mary Ecke, Yoshiyuki Fukuda, Antonio Martinez-Sanchez, Wolfgang Baumeister, Günther Gerisch
Morphology of mitochondria in spatially restricted axons revealed by cryo-electron tomography
Neurons project axons to local and distal sites and can display heterogeneous morphologies with limited physical dimensions that may influence the structure of large organelles such as mitochondria. Using cryo-electron tomography (cryo-ET), we characterized native environments within axons and presynaptic varicosities to examine whether spatial restrictions within these compartments influence the morphology of mitochondria. Segmented tomographic reconstructions revealed distinctive morphologi... Read more
Tara D. Fischer, Pramod K. Dash, Jun Liu, M. Neal Waxham
Centrioles are vital cellular structures that form centrosomes and cilia. The formation and function of cilia depends on a set of centriole’s distal appendages. In this study, we use correlative super resolution and electron microscopy to precisely determine where distal appendage proteins localize in relation to the centriole microtubules and appendage electron densities. Here we characterize a novel distal appendage protein ANKRD26 and detail, in high resolution, the initial steps of dist... Read more
Mathew Bowler, Dong Kong, Shufeng Sun, Rashmi Nanjundappa, Lauren Evans, Veronica Farmer, Andrew Holland, Moe R. Mahjoub, Haixin Sui & Jadranka Loncarek
Serial block face scanning electron microscopy (SBF-SEM) is a powerful method to analyze cells in 3D. Here, working at the resolution limit of the method, we describe a correlative light–SBF-SEM workflow to resolve microtubules of the mitotic spindle in human cells. We present four examples of uses for this workflow that are not practical by light microscopy and/or transmission electron microscopy. First, distinguishing closely associated microtubules within K-fibers; second, resolving brid... Read more
Faye M. Nixon, Thomas R. Honnor, Nicholas I. Clarke, Georgina P. Starling, Alison J. Beckett, Adam M. Johansen, Julia A. Brettschneider, Ian A. Prior, Stephen J. Royle
Chromosome segregation occurs by microtubule pushing in oocytes
During cell division, spindle microtubules ensure an equal repartition of chromosomes between the two daughter cells. While the kinetochore-dependent mechanisms that drive mitotic chromosome segregation are well understood, in oocytes of most species atypical spindles assembled in absence of centrosomes entail poorly understood mechanisms of chromosome segregation. In particular, the structure(s) responsible for force generation during meiotic chromosome separation in oocytes is unclear. Usin... Read more
Kimberley Laband, Rémi Le Borgne, Frances Edwards, Marine Stefanutti, Julie C. Canman, Jean-Marc Verbavatz, Julien Dumont
Microstructure analysis and image-based modelling of face masks for COVID-19 virus protection
Until March 2021, around 120 million coronavirus disease (COVID-19) infected cases and over 2.6 million deaths have been reported worldwide. […] Recent investigations have implied that face masks help to reduce the disease transmission and therefore slow down the growth of the epidemic curve. However, there are still ongoing debates on the efficacy of wearing masks […] since there is a general lack of information relating to the material structure of commonly used face masks.Read more
Wenjia Du, Francesco Iacoviello, Tacson Fernandez, Rui Loureiro, Daniel J. L. Brett & Paul R. Shearing