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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Intravital microscopy provides dynamic understanding of multiple cell biological processes, but its limited resolution has so far precluded structural analysis. Because it is difficult to capture rare and transient events, only a few attempts have been made to observe specific developmental and pathological processes in animal models using electron microscopy. The multimodal correlative approach that we propose here combines intravital microscopy, microscopic X-ray computed tomography and thr... Read more
Matthia A. Karreman, Luc Mercier, Nicole L. Schieber, Gergely Solecki, Guillaume Allio, Frank Winkler, Bernhard Ruthensteiner, Jacky G. Goetz, Yannick Schwab
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
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
Tobacco use is associated with an increased risk of hearing loss in older individuals, suggesting cigarette smoke (CS) exposure may target the peripheral auditory organs. However, the effects of CS exposure on general cochlear anatomy have not previously been explored.
Here we compare control and chronic CS exposed cochleae from adult mice to assess changes in structure and cell survival. Two-photon imaging techniques, including the imaging of second harmonic generation (SHG) and two-p... Read more
Stephen T. Paquette, Ryan P. Dawes, Isaac K. Sundar, Irfan Rahman, Edward B. Brown & Patricia M. White
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 mitochondrial... Read more
Hero Robles, SungJae Park, Matthew S. Joens, James A.J. Fitzpatrick, Clarissa S. Craft, Erica L. Scheller
Cranial ornaments such as keratinous horns and bony casques are commonplace amongst birds and take a variety of diverse forms. Possible functions include display, thermoregulation, vocalisation and intraspecific combat, yet few hypotheses have been directly tested. Here we investigate the anatomy and mechanics of the casque of the Southern Cassowary (Casuarius casuarius), and test functional hypotheses using CT-based virtual dissection.
In particular, we determine the nature of pneumat... Read more
Charlotte A. Brassey , Thomas O’Mahoney
Understanding amazingly complex brain functions and pathologies requires a complete cerebral vascular atlas in stereotaxic coordinates. Making a precise atlas for cerebral arteries and veins has been a century-old objective in neuroscience and neuropathology. Using micro-optical sectioning tomography (MOST) with a modified Nissl staining method, we acquired five mouse brain data sets containing arteries, veins, and microvessels. Based on the brain-wide vascular spatial structures and brain re... Read more
Benyi Xiong, Anan Li, Yang Lou, Shangbin Chen, Ben Long, Jie Peng, Zhongqin Yang, Tonghui Xu, Xiaoquan Yang, Xiangning Li, Tao Jiang, Qingming Luo and Hui Gong
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
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
Endosseous oral implant is applied for orthodontic anchorage in subjects with multiple tooth agenesis. Its effectiveness under orthodontic loading has been demonstrated clinically and experimentally. This study investigates the deformation and stress on the bone and implant for different bite forces by three-dimensional (3D) finite element (FE) methods. A numerical simulation of deformation and stress distributions around implants was used to estimate the survival life for implants. The model... Read more
Hsin-Chung Cheng, Boe-Yu Peng, May-Show Chen, Chiung-Fang Huang, Yi Lin, and Yung-Kang Shen
The sequential activation of neurons has been observed in various areas of the brain, but in no case is the underlying network structure well understood. Here we examined the circuit anatomy of zebra finch HVC, a cortical region that generates sequences underlying the temporal progression of the song. We combined serial block-face electron microscopy with light microscopy to determine the cell types targeted by HVC(RA) neurons, which control song timing. Close to their soma, axons... Read more
Jörgen Kornfeld, Sam E Benezra, Rajeevan T Narayanan, Fabian Svara, Robert Egger, Marcel Oberlaender, Winfried Denk, Michael A Long
The human head can be subjected to numerous impact loadings such as those produced by a fall or during sport activities. These accidents can result in skull fracture and in some complex cases, part of the skull may need to be replaced by a biomedical implant. Even when the skull is not damaged, such accidents can result in brain swelling treated by decompressive craniectomy. Usually, after recovery, the part of the skull that has been removed is replaced by a prosthesis. In such situations, a... Read more
D. Garcia-Gonzalez, J. Jayamohan, S.N.Sotiropoulos, S.-H.Yoon, J.Cook, C.R.Siviour, A.Arias, A.Jérusalem
We demonstrate that phase retrieval and tomographic imaging at the organ level of small animals can be advantageously carried out using the monochromatic radiation emitted by a compact x-ray light source, without further optical elements apart from source and detector. This approach allows to carry out microtomography experiments which – due to the large performance gap with respect to conventional laboratory instruments – so far were usually limited to synchrotron sources. We dem... Read more
Mareike Töpperwien, Regine Gradl, Daniel Keppeler, Malte Vassholz, Alexander Meyer, Roland Hessler, Klaus Achterhold, Bernhard Gleich, Martin Dierolf, Franz Pfeiffer, Tobias Moser & Tim Salditt
The beating heart is known to produce pressure and airflow oscillations in the lungs of mammals. This phenomenon is often disregarded as detailed measurement of its effects in the lung have hitherto not been possible. Previous studies have attempted to measure the effect of these oscillations on gas mixing. However, the results have proven inconclusive, due to the lack of a direct measurement tool capable of flow measurement throughout the entire bronchial tree. Here we present the first deta... Read more
Stephen Dubsky, Jordan Thurgood, Andreas Fouras, Bruce R. Thompson & Gregory J. Sheard
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…Read more
Louise Hughes, Samantha Borrett, Katie Towers, Tobias Starborg, Sue Vaughan
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
Acidic microenvironments created by bacterial clusters thriving in a polysaccharide matrix could be behind localized tooth decay. Jin Xiao of the University of Rochester Medical Center and Geelsu Hwang of the University of Pennsylvania with colleagues in the US mapped acidity changes across tooth enamel caused by the microstructure of dental plaque: a film of bacteria and the polysaccharide matrix they secrete. Using fluorescence microscopy, they studied the 3D architecture of plaque that for... Read more
Jin Xiao, Anderson T Hara, Dongyeop Kim, Domenick T Zero, Hyun Koo et al.
Despite the progress made in selective plane illumination microscopy, high-resolution 3D live imaging of multicellular specimens remains challenging. Tiling light-sheet selective plane illumination microscopy (TLS-SPIM) with real-time light-sheet optimization was developed to respond to the challenge…Read more
Qinyi Fu, Benjamin L. Martin, David Q. Matus, Liang Gao
Correlative light and electron microscopy (CLEM) is a powerful approach to investigate the molecular ultrastructure of labeled cell compartments. However, quantitative CLEM studies are rare, mainly due to small sample sizes and the sensitivity of fluorescent proteins to strong fixatives and contrasting reagents for EM. Here, we show that fusion of…Read more
Andreas Müller, Martin Neukam, Anna Ivanova, Anke Sönmez, Carla Münster, Susanne Kretschmar, Yannis Kalaidzidis, Thomas Kurth, Jean-Marc Verbavatz & Michele Solimena