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.
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.
Immunofluorescence tomography is a high-resolution 3-D reconstruction method based on methacrylate embedding and serial-sectioning, where 2-D images of immuno-stained serial-sections are computationally aligned into image stacks, and the 3-D volume rendered. Butyl-Methyl Methacrylate (BMMA) plastic was adopted as it preserves excellent tissue morphology and can be de-plasticized easily using an organic solvent, which enables immuno-staining of serial-sections without antibody penetration issu... Read more
Parfitt, Geraint J
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
Salmonella Typhimurium (S.Tm) is an enteropathogen requiring multiple virulence factors, including two type three secretion systems (T1 and T2). T1 triggers epithelium invasion in which the bacteria are taken up into endosomes that mature into Salmonella-containing vacuoles (SCV) and trigger T2 induction upon acidification. Mechanisms controlling endosome membrane integrity or pathogen egress into the cytosol are incompletely understood. We screened for host factors affecting invasion and SCV... Read more
Saskia Kreibich, Mario Emmenlauer, Jennifer Fredlund, Pauli Rämö, Christian Münz, Christoph Dehio, Jost Enninga, Wolf-Dietrich Hardt
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
Deep brain stimulation (DBS) requires accurate localization of the anatomical target structure, and the precise placement of the DBS electrode within it. Ultra-high field 7 Tesla (T) MR images can be utilized to create patient-specific anatomical 3D models of the subthalamic nuclei (STN) to enhance pre-surgical DBS targeting as well as post-surgical visualization of the DBS lead position and orientation. We validated the accuracy of the 7T imaging-based patient-specific model of the STN and m... Read more
Yuval Duchin, Reuben R. Shamir, Remi Patriat, Jinyoung Kim, Jerrold L. Vitek, Guillermo Sapiro, Noam Harel
Dense calcium caseinate dispersions can be transformed into hierarchically ﬁbrous structures by shear deformation. This transformation can be attributed to the intrinsic properties of calcium caseinate. Depending on the dispersion preparation method, a certain amount of air gets entrapped in the sheared protein matrix. Although anisotropy is obtained in the absence of entrapped air, the ﬁbrous appearance and mechanical anisotropy of the calcium caseinate materials are more pronounced with... Read more
Zhaojun Wang, Bei Tian, Remko Boom, Atze Jan van der Goot
Catalyst aging effects were analyzed using X-ray absorption micro-computed tomography in combination with conventional characterization methods on various length scales ranging from nm to μm to gain insight into deactivation mechanisms.
For this purpose, a 4 wt% Pt/Al2O3 model exhaust gas catalyst was coated on a cordierite honeycomb and subjected to sequential thermal aging in static air at 950 °C for 4, 8, 12 and 24 hours. The ag... Read more
Georg Hofmann, Amélie Rochet, Elen Ogel, Maria Casapu, Stephan Ritter, Malte Ogurreck and Jan-Dierk Grunwaldt
Composite cathodes comprising nanoscale
powders are expected to impart with high specific surface
area and triple phase boundary (TPB) density, which will lead
to better performance.
However, uniformly mixing nanosized heterophase powders remains a challenge due to their high surface energy and thus ease with which they agglomerate into their individual phases during the mixing and sintering
processes. In this study, we successfully synthesized La0.6Sr0.4Co0.2Fe... Read more
Dong Woo Joh, Areum Cha, Jeong Hwa Park, Kyeong Joon Kim, Kyung Taek Bae, Doyeub Kim, Young Ki Choi, Hyegsoon An, Ji Su Shin, Kyung Joong Yoon, and Kang Taek Lee
Phylactolaemate bryozoans are the sister-group to all remaining bryozoan taxa. Consequently, their study is essential to reveal and analyze ancestral traits of Phylactolaemata and Bryozoa in general.
They are the only bryozoans to possess an epistome which traditionally has been regarded as shared with phoronids and brachiopods. Contrary to older observations, an epistome was recently reported to be missing in the early branching phylactolaemate Lophopus crystallinus. In this... Read more
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
Electrospun all-fiber flexible supercapacitor with nanofiber electrodes/separator.
- Increased graphitic degree with the addition of MnACAC and thermal decomposition.
- Enhanced capacitive performance with the addition of MnO.
- Quantified nanofiber alignment and increased bias with MnO over undoped fibers.
- FIBSEM tomography of nanofibers showing MnO disitribution in carbon nanofibers.
We present an all-fiber flexible supercapacitor with compo... Read more
Xinhua Liu, Max Naylor Marlow, Samuel J. Cooper, Bowen Song, Xiaolong Chen, Nigel P. Brandon, Billy Wu
We present an in vivo confocal laser scanning microscopy based method for large 3D reconstruction of the cornea on a cellular level with cropped volume sizes up to 266 x 286x 396 µm3.
The microscope objective used is equipped with a piezo actuator for automated, fast and precise closed-loop focal plane control. Furthermore, we present a novel concave surface contact cap, which significantly reduces eye movements by up to 87%, hence increasing the overlapping image area of the whole st... Read more
Sebastian Bohn, Karsten Sperlich, Stephan Allgeier, Andreas Bartschat, Ruby Prakasam, Klaus-martin Reichert, Heinrich Stolz, Rudolf Guthoff, Ralf Mikut, Bernd Köhler, and Oliver Stachs
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
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