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.

Fragmentation of wall rock garnets during deep crustal earthquakes

Fragmentation of wall rock garnets during deep crustal earthquakes

Deformation of the lithosphere by seismic slip along faults dissipates energy to the immediate surroundings as heat and elastic waves. Heat effects may occasionally cause frictional melting along the slip plane, leading to the formation of pseudotachylite, a characteristic fine-grained or glassy fault rock, interpreted as the quenched melt. Recently, it has been suggested that mechanical effects due to rapid loading, such as the formation of shiny “mirror” surfaces or pulverization of roc... Read more

Department of Geosciences, University of Oslo; Department of Earth Sciences, Utrecht University; Géosciences Montpellier, Université de Montpellier; Debye Institute for Nanomaterials Science, Utrecht University

Read full paper
Characterization of the Interface Between Coating and Fibrous Layers of Paper

Characterization of the Interface Between Coating and Fibrous Layers of Paper

Coated paper is an example of a multi-layer porous medium, involving a coating layer along the two surfaces of the paper and a fibrous layer in the interior of the paper. The interface between these two media needs to be characterized in order to develop relevant modeling tools. After careful cutting of the paper, a cross section was imaged using focused ion beam scanning electron microscopy. The resulting image was analyzed to characterize the coating layer and its transition to the fibrous ... Read more

H. Aslannejad, S. M. Hassanizadeh, M. A. Celia

Read full paper
High-Resolution 3D FIB-SEM Image Analysis and Validation of Numerical Simulations of Nanometre-Scale Porous Ceramic with Comparisons to Experimental Results

High-Resolution 3D FIB-SEM Image Analysis and Validation of Numerical Simulations of Nanometre-Scale Porous Ceramic with Comparisons to Experimental Results

The development of focused ion beam-scanning electron microscopy (FIB-SEM) techniques has allowed high-resolution 3D imaging of nanometre-scale porous materials. These systems are of important interest to the oil and gas sector, as well as for the safe long-term storage of carbon and nuclear waste. This work focuses on validating the accurate representation of sample pore space in FIB-SEM-reconstructed volumes and the predicted permeability of these systems from subsequent single-phase flow s... Read more

Department of Chemical Engineering, Qatar Carbonates and Carbon Storage Research Centre, Imperial College London | Department of Applied Mathematics and Theoretical Physics, Cambridge University

Read full paper
Deep nuclear invaginations are linked to cytoskeletal filaments – integrated bioimaging of epithelial cells in 3D culture

Deep nuclear invaginations are linked to cytoskeletal filaments – integrated bioimaging of epithelial cells in 3D culture

The importance of context in regulation of gene expression is now an accepted principle; yet the mechanism by which the microenvironment communicates with the nucleus and chromatin in healthy tissues is poorly understood. A functional role for nuclear and cytoskeletal architecture is suggested by the phenotypic differences observed between epithelial and mesenchymal cells…

Read more

Danielle M. Jorgens, Jamie L. Inman, Michal Wojcik, Claire Robertson, Hildur Palsdottir, Wen-Ting Tsai, Haina Huang, Alexandre Bruni-Cardoso, Claudia S. López, Mina J. Bissell, Ke Xu, Manfred Auer

Read full paper
Macropinosomes are key players in early shigella invasion and vacuolar escape in epithelial cells

Macropinosomes are key players in early shigella invasion and vacuolar escape in epithelial cells

Intracellular pathogens include all viruses, many bacteria and parasites capable of invading and surviving within host cells. Key to survival is the subversion of host cell pathways by the pathogen for the purpose of propagation and evading the immune system. The intracellular bacterium Shigella flexneri, the causative agent of bacillary dysentery, invades host cells in a vacuole that is subsequently ruptured to allow growth of the pathogen within the host cytoplasm…

Read more

Allon Weiner , Nora Mellouk , Noelia Lopez-Montero , Yuen-Yan Chang, Célia Souque, Christine Schmitt, Jost Enninga

Read full paper
Ultrastructural Characterization of Flashing Mitochondria

Ultrastructural Characterization of Flashing Mitochondria

Mitochondria undergo spontaneous transient elevations in matrix pH associated with drops in mitochondrial membrane potential. These mitopHlashes require a functional respiratory chain and the profusion protein optic atrophy 1, but their mechanistic basis is unclear. To gain insight on the origin of these dynamic events, we resolved the ultrastructure of flashing mitochondria by correlative light and electron microscopy. HeLa cells expressing the matrix-targeted pH probe mitoSypHer were screen... Read more

Manon Rosselin, Paula Nunes-Hasler, and Nicolas Demaurex

Read full paper
Morphological process of podocyte development revealed by block-face scanning electron microscopy

Morphological process of podocyte development revealed by block-face scanning electron microscopy

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…

Read more

Koichiro Ichimura, Soichiro Kakuta, Yuto Kawasaki, Takayuki Miyaki, Takahiro Nonami, Naoyuki Miyazaki, Tomoyo Nakao, Sakiko Enomoto, Shigeo Arai, Masato Koike, Kazuyoshi Murata, Tatsuo Sakai

Read full paper
Correlative cryo-electron microscopy reveals the structure of TNTs in neuronal cells

Correlative cryo-electron microscopy reveals the structure of TNTs in neuronal 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

Anna Sartori-Rupp, Diégo Cordero Cervantes, Anna Pepe, Karine Gousset, Elise Delage, Simon Corroyer-Dulmont, Christine Schmitt, Jacomina Krijnse-Locker & Chiara Zurzolo

Read full paper
Partial dissolution of carbonate rock grains during reactive CO2-saturated brine injection under reservoir conditions

Partial dissolution of carbonate rock grains during reactive CO2-saturated brine injection under reservoir conditions

Our novel procedure of injecting oil after reactive transport has revealed previously unidentified (ghost) regions of partially-dissolved grains of carbonate rock. X-ray micro-tomography and FIB-SEM techniques were used to identify and resolve these ghost regions in three-dimensions at the nm- to µm-scale. Considering the solid part of the ghost regions as macro (bulk) pore space can result in the overestimation of porosity and permeability predi... Read more

Kamaljit Singh , Benaiah U. Anabaraonye , Martin J. Blunt , John Crawshaw

Read full paper
STIM1 promotes migration, phagosomal maturation and antigen cross-presentation in dendritic cells

STIM1 promotes migration, phagosomal maturation and antigen cross-presentation in dendritic cells

Antigen cross-presentation by dendritic cells (DC) stimulates cytotoxic T cell activation to promote immunity to intracellular pathogens, viruses and cancer. Phagocytosed antigens generate potent T cell responses, but the signalling and trafficking pathways regulating their cross-presentation are unclear. Here, we show that ablation of the store-operated-Ca2+-entry regulator STIM1 in mouse myeloid cells impairs cross-presentation and DC migration in vivo and in vitro. Stim1... Read more

Paula Nunes-Hasler, Sophia Maschalidi, Carla Lippens, Cyril Castelbou, Samuel Bouvet, Daniele Guido, Flavien Bermont, Esen Y. Bassoy, Nicolas Page, Doron Merkler, Stéphanie Hugues, Denis Martinvalet, Bénédicte Manoury & Nicolas Demaurex

Read full paper
Enhanced mechanical stability of Ni-YSZ scaffold demonstrated by nanoindentation and Electrochemical Impedance Spectroscopy

Enhanced mechanical stability of Ni-YSZ scaffold demonstrated by nanoindentation and Electrochemical Impedance Spectroscopy

The electrochemical performance of Ni-YSZ SOFC anodes can quickly degrade during redox cycling. Mechanical damage at interfaces significantly decreases the number of active triple phase boundaries. This study firstly focuses on the sintering temperature impact on YSZ scaffold mechanical properties. The YSZ scaffold sintered at 1200 °C exhibited 56% Read more

B.Song; E.Ruiz-Trejo; N.P.Brandon

Read full paper
Quantification of the degradation of Ni-YSZ anodes upon redox cycling

Quantification of the degradation of Ni-YSZ anodes upon redox cycling

Ni-YSZ anodes for Solid Oxide Fuel Cells are vulnerable to microstructural damage during redox cycling leading to a decrease in the electrochemical performance.

 

  • Quantification of redox damage by coupling 3D tomography, EIS and nanoindentation.
  • YSZ fracture, Ni detachment and agglomeration led to irreversible mechanical damage.
  • Ni nanoparticles obtained upon redox cycling improve electrochemical performance.
  • Loss in TPB densi... Read more

Bowen Song, Enrique Ruiz-Trejo, Antonio Bertei, Nigel P.Brandon

Read full paper
Multi-length scale tomography for the determination and optimization of the effective microstructural properties in novel hierarchical solid oxide fuel cell anodes

Multi-length scale tomography for the determination and optimization of the effective microstructural properties in novel hierarchical solid oxide fuel cell anodes

Our parametric study shows that increasing the porosity in the spongy layer beyond 10% enhances the effective transport parameters of the spongy layer at an exponential rate, but linearly for the full anode. For the first time, local and global mass transport properties are correlated to the microstructure, which is of wide interest for rationalizing the design optimization of SOFC electrodes and more generally for hierarchical materials in batteries and membranes.

Read more

Xuekun Lu, Oluwadamilola O. Taiwo, Antonio Bertei, Tao Li, Kang Li, Dan J.L. Brett, Paul R.Shearing

Read full paper
Analysis of Void Volume in Composite Electrode of All-solid-state Lithium-ion Battery Employing FIB-SEM and Union Operation Image Processing

Analysis of Void Volume in Composite Electrode of All-solid-state Lithium-ion Battery Employing FIB-SEM and Union Operation Image Processing

We had proposed an image-processing scheme using union operation suitable for extracting target features with hierarchical dimensions from the original data, and applied it to void analysis in a composite electrode of an all-solid-state lithium ion battery (LIB). Void analysis is very important in developing better composite electrodes for all-solid-state LIBs because internal voids should increase the interfacial resistance. Film formation of electrode-solid electrolyte composites by the aer... Read more

Yuta Yamamoto , Yasutoshi Iriyama, and Shunsuke Muto

Read full paper
Enhanced Imaging of Lithium Ion Battery Electrode Materials

Enhanced Imaging of Lithium Ion Battery Electrode Materials

The authors present for the first time a new methodology of contrast enhancement for 3D imaging, including novel advanced quantification, on a commercial Lithium Iron Phosphate (LFP) LiFePO4 cathode. The aim of this work is to improve the quality of the 3D imaging of challenging battery materials by developing methods to increase contrast between otherwise previously poorly differentiated phases. This is necessary to enable capture of the real geometry of electrode microstructures... Read more

Moshiel Biton, Vladimir Yufit, Farid Tariq, Masashi Kishimoto and Nigel Brandon

Read full paper
A multi-scale correlative investigation of ductile fracture

A multi-scale correlative investigation of ductile fracture

The use of novel multi-scale correlative methods, which involve the coordinated characterization of matter across a range of length scales, are becoming of increasing value to materials scientists. Here, we describe for the first time how a multi-scale correlative approach can be used to investigate the nature of ductile fracture in metals. Specimens of a nuclear pressure vessel steel, SA508 Grade 3, are examined following ductile fracture using medium and high-resolution 3D X-ray computed to... Read more

School of Materials, University of Manchester; National Nuclear Laboratory; BAM Federal Institute for Materials Research and Testing; Thermo Fischer Scientific

Read full paper