Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues
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Type
ArticleAuthors
Cali, CorradoBaghabrah, Jumana
Boges, Daniya
Holst, Glendon
Kreshuk, Anna
Hamprecht, Fred A.
Srinivasan, Madhusudhanan
Lehväslaiho, Heikki
Magistretti, Pierre J.

KAUST Department
Biological and Environmental Sciences and Engineering (BESE) DivisionBioscience Program
Computer Science Program
KAUST Visualization Laboratory (KVL)
Visualization
Date
2015-08-11Online Publication Date
2015-08-11Print Publication Date
2016-01-01Permanent link to this record
http://hdl.handle.net/10754/561070
Metadata
Show full item recordAbstract
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 NeurologyPublisher
WileyJournal
Journal of Comparative NeurologyPubMed ID
26179415Additional Links
http://doi.wiley.com/10.1002/cne.23852ae974a485f413a2113503eed53cd6c53
10.1002/cne.23852
Scopus Count
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