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    Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues

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    Type
    Article
    Authors
    Cali, Corrado
    Baghabrah, Jumana
    Boges, Daniya
    Holst, Glendon
    Kreshuk, Anna
    Hamprecht, Fred A.
    Srinivasan, Madhusudhanan
    Lehväslaiho, Heikki
    Magistretti, Pierre J. cc
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Program
    Computer Science Program
    KAUST Visualization Laboratory (KVL)
    Visualization
    Date
    2015-08-11
    Online Publication Date
    2015-08-11
    Print Publication Date
    2016-01-01
    Permanent link to this record
    http://hdl.handle.net/10754/561070
    
    Metadata
    Show full item record
    Abstract
    Advances for application of electron microscopy to serial imaging are opening doors to new ways of analyzing cellular structure. New and improved algorithms and workflows for manual and semiautomated segmentation allow to observe the spatial arrangement of the smallest cellular features with unprecedented detail in full three-dimensions (3D). From larger samples, higher complexity models can be generated; however, they pose new challenges to data management and analysis. Here, we review some currently available solutions and present our approach in detail. We use the fully immersive virtual reality (VR) environment CAVE (cave automatic virtual environment), a room where we are able to project a cellular reconstruction and visualize in 3D, to step into a world created with Blender, a free, fully customizable 3D modeling software with NeuroMorph plug-ins for visualization and analysis of electron microscopy (EM) preparations of brain tissue. Our workflow allows for full and fast reconstructions of volumes of brain neuropil using ilastik, a software tool for semiautomated segmentation of EM stacks. With this visualization environment, we can walk into the model containing neuronal and astrocytic processes to study the spatial distribution of glycogen granules, a major energy source that is selectively stored in astrocytes. The use of CAVE was key to observe a nonrandom distribution of glycogen, and led us to develop tools to quantitatively analyze glycogen clustering and proximity to other subcellular features. This article is protected by copyright. All rights reserved.
    Citation
    Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues 2015:n/a Journal of Comparative Neurology
    Publisher
    Wiley
    Journal
    Journal of Comparative Neurology
    DOI
    10.1002/cne.23852
    PubMed ID
    26179415
    Additional Links
    http://doi.wiley.com/10.1002/cne.23852
    ae974a485f413a2113503eed53cd6c53
    10.1002/cne.23852
    Scopus Count
    Collections
    Articles; Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Computer Science Program; KAUST Visualization Laboratory (KVL)

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