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 is used to address various scientific and industrial research topics.
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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
While fluorescence microscopy provides tools for highly specific labeling and sensitive detection, its resolution limit and lack of general contrast has hindered studies of cellular structure and protein localization. Recent advances in correlative light and electron microscopy (CLEM), including the fully integrated CLEM workflow instrument, the FEI CorrSight with MAPS, have allowed for a more reliable, reproducible, and quicker approach to correlate three-dimensional time-lapse confocal fluo... Read more
Claudia S. Lopez, Cedric Bouchet-Marquis, Christopher P. Arthur, Jessica L. Riesterer, Gregor Heiss, Guillaume Thibault, Lee Pullan, Sunjong Kwon, Joe W. Gray
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
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
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
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
Unlike white and brown adipose tissues, the bone marrow adipocyte (BMA) exists in a microenvironment containing unique populations of hematopoietic and skeletal cells.
To study this microenvironment at the subcellular level, we performed a three-dimensional analysis of the ultrastructure of the BMA niche with focused ion beam scanning electron microscopy (FIB-SEM). This revealed that BMAs display hallmarks of metabolically active cells including polarized lipid deposits, a dense mitoch... Read more
Hero Robles, SungJae Park, Matthew S. Joens, James A.J. Fitzpatrick, Clarissa S. Craft, Erica L. Scheller
Chromosomal instability is a hallmark of cancer and correlates with the presence of extra centrosomes, which originate from centriole overduplication.
Overduplicated centrioles lead to the formation of centriole rosettes, which mature into supernumerary centrosomes in the subsequent cell cycle. While extra centrosomes promote chromosome missegregation by clustering into pseudo-bipolar spindles, the contribution of centriole rosettes to chromosome missegregation is unknown. We us... Read more
Marco R.Cosenza, Anna Cazzola, Annik Rossberg, Nicole L. Schieber, Gleb Konotop, Elena Bausch, Alla Slynko, Tim Holland-Letz, Marc S.Raab, Taronish Dubash, Hanno Glimm, Sven Poppelreuther, Christel Herold-Mende, Yannick Schwab, Alwin Krämer
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
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
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
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
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
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
Advanced nanotomographic analysis is still far from routine, and a number of challenges remain in data acquisition and post-processing. In this work, we present a number of techniques to improve the quality of the acquired data, together with easy-to-implement methods to obtain “advanced” microstructural quantifications. The techniques are applied to a solid oxide fuel cell cathode of interest to the electrochemistry community, but the methodologies are easily adaptable to a wide range of... Read more
Joshua A.Taillon, Christopher Pellegrinelli, Yi-Lin Huang, Eric D.Wachsman, Lourdes G. Salamanca-Riba
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
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