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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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
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
Bacteria of the phylum Planctomycetes have been previously reported to possess several features that are typical of eukaryotes, such as cytosolic compartmentalization and endocytosis-like macromolecule uptake. However, recent evidence points towards a Gram-negative cell plan for Planctomycetes, although in-depth experimental analysis has been hampered by insufficient genetic tools…Read more
Christian Boedeker, Margarete Schüler, Greta Reintjes, Olga Jeske, Muriel C. F. van Teeseling et al.
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
With the advent of neurogenetic methods, the neural basis of behavior is presently being analyzed in more and more detail. This is particularly true for visually driven behavior of Drosophila melanogaster where cell-specific driver lines exist that, depending on the combination with appropriate effector genes, allow for targeted recording, silencing and optogenetic stimulation of individual cell-types. Together with detailed connectomic data of large parts of the fly optic lobe, this has rece... Read more
Kevin M. Boergens , Christoph Kapfer, Moritz Helmstaedter, Winfried Denk, Alexander Borst
Analysis of neuronal arborization and connections is a powerful tool in fundamental and clinical neuroscience. Changes in neuronal morphology are central to brain development and plasticity and are associated with numerous diseases. Golgi staining is a classical technique based on a deposition of metal precipitate in a random set of neurons. Despite their versatility, Golgi methods have limitations that largely precluded their use in advanced microscopy. We combined Golgi staining with fluore... Read more
Katlijn Vints, Dorien Vandael, Pieter Baatsen, Benjamin Pavie, Frank Vernaillen, Nikky Corthout, Vasily Rybakin, Sebastian Munck & Natalia V. Gounko
The mitotic spindle ensures the faithful segregation of chromosomes. Here we combine the first large-scale serial electron tomography of whole mitotic spindles in early C. elegans embryos with live-cell imaging to reconstruct all microtubules in 3D and identify their plus- and minus-ends. We classify them as kinetochore (KMTs), spindle (SMTs) or astral microtubules (AMTs) according to their positions, and quantify distinct properties of each class. While our light microscopy and muta... Read more
Stefanie Redemann, Johannes Baumgart, Norbert Lindow, Michael Shelley, Ehssan Nazockdast, Andrea Kratz, Steffen Prohaska, Jan Brugués, Sebastian Fürthauer & Thomas Müller-Reichert
In biomedical research, a huge variety of different techniques is currently available for the structural examination of small specimens, including conventional light microscopy (LM), transmission electron microscopy (TEM), confocal laser scanning microscopy (CLSM), microscopic X-ray computed tomography (microCT), and many others. Since every imaging method is physically limited by certain parameters, a correlative use of complementary methods often yields a significant broader range of inform... Read more
Stephan Handschuh, Natalie Baeumler, Thomas Schwaha and Bernhard Ruthensteiner
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 mitosis, the centrosome expands its capacity to nucleate microtubules. Understanding the mechanisms of centrosomal microtubule nucleation is, however, constrained by a lack of knowledge of the amount of soluble and polymer tubulin at mitotic centrosomes. Here we combined light microscopy and serial-section electron tomography to measure the amount of dimer and polymer at mitotic centrosomes in early C. elegans embryos. We show that a C. elegans one-cell stage centrosome at metaphase co... Read more
Johannes Baumgart, Marcel Kirchner, Stefanie Redemann, Jeffrey Woodruff, Jean-Marc Verbavatz, Frank Julicher, Anthony Hyman, Thomas Mueller-Reichert, Jan Brugues
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
Human skeletal remains from archaeological contexts occasionally present signs of traumatic injuries from weapons, revealing, for example, the degree of interpersonal violence, the type of weapon and the sequence of events of a specific historical context.
Traumatic lesions are generally analyzed using macroscopic and microscopic methods, which are not necessarily integrated in the same study. In this study, we employed a multi-analytical approach to determine i... Read more
Antonino Vazzana, Lucia Martina Scalise, Mirko Traversari, Carla Figus, Salvatore Andrea Apicella, Laura Buti, Gregorio Oxilia, Rita Sorrentino, Silvia Pellegrini, Chiara Matteucci, Lucio Calcagnile, Raffaele Savigni, Robin N.M.Feeney, Giorgio Gruppioni, Stefano Benazziah
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 ∼3.48 billion-year-old Dresser Formation, Pilbara Craton, Western Australia, is a key geological unit for the study of Earth’s earliest life and the habitats it occupied. Here, we describe a new suite of spheroidal to lenticular microstructures that morphologically resemble some previously reported Archean microfossils. Correlative microscopy shows that these objects have a size distribution, wall ultrastructure, and chemistry that are incompatible with a microfossil origin and in... Read more
Wacey David , Noffke Nora , Saunders Martin , Guagliardo Paul , and Pyle David M