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

Handle URI:
http://hdl.handle.net/10754/561070
Title:
Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues
Authors:
Cali, Corrado; Baghabrah, Jumana; Boges, Daniya; Holst, Glendon; Kreshuk, Anna; Hamprecht, Fred A.; Srinivasan, Madhusudhanan; Lehväslaiho, Heikki; Magistretti, Pierre J. ( 0000-0002-6678-320X )
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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; KAUST Visualization Laboratory (KVL)
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-Blackwell
Journal:
Journal of Comparative Neurology
Issue Date:
14-Jul-2015
DOI:
10.1002/cne.23852
Type:
Article
ISSN:
00219967
Additional Links:
http://doi.wiley.com/10.1002/cne.23852
Appears in Collections:
Articles; KAUST Visualization Laboratory (KVL); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorCali, Corradoen
dc.contributor.authorBaghabrah, Jumanaen
dc.contributor.authorBoges, Daniyaen
dc.contributor.authorHolst, Glendonen
dc.contributor.authorKreshuk, Annaen
dc.contributor.authorHamprecht, Fred A.en
dc.contributor.authorSrinivasan, Madhusudhananen
dc.contributor.authorLehväslaiho, Heikkien
dc.contributor.authorMagistretti, Pierre J.en
dc.date.accessioned2015-07-27T12:30:02Zen
dc.date.available2015-07-27T12:30:02Zen
dc.date.issued2015-07-14en
dc.identifier.citationThree-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues 2015:n/a Journal of Comparative Neurologyen
dc.identifier.issn00219967en
dc.identifier.doi10.1002/cne.23852en
dc.identifier.urihttp://hdl.handle.net/10754/561070en
dc.description.abstractAdvances 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.en
dc.publisherWiley-Blackwellen
dc.relation.urlhttp://doi.wiley.com/10.1002/cne.23852en
dc.rightsThis is the peer reviewed version of the following article: Calì, Corrado, Jumana Baghabra, Daniya J. Boges, Glendon R. Holst, Anna Kreshuk, Fred A. Hamprecht, Madhusudhanan Srinivasan, Heikki Lehväslaiho, and Pierre J. Magistretti. "Three‐dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues." Journal of Comparative Neurology (2015), which has been published in final form at http://doi.wiley.com/10.1002/cne.23852. This article may be used for non-commercial purposes in accordance With Wiley Terms and Conditions for self-archiving.en
dc.subjectGlycogen clusteringen
dc.subjectglycogen spatial distributionen
dc.subject3D navigationen
dc.subject3D analysisen
dc.subjectvolume analysisen
dc.subjectfast 3D reconstructionen
dc.titleThree-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissuesen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentKAUST Visualization Laboratory (KVL)en
dc.identifier.journalJournal of Comparative Neurologyen
dc.eprint.versionPost-printen
dc.contributor.institutionHeidelberg Collaboratory for Image Processing (HCI); University of Heidelberg; Heidelberg Germanyen
dc.contributor.institutionBrain Mind Institute, EPFL, Lausanne, Switzerlanden
kaust.authorCali, Corradoen
kaust.authorMagistretti, Pierre J.en
kaust.authorBaghabrah, Jumanaen
kaust.authorBoges, Daniyaen
kaust.authorHolst, Glendonen
kaust.authorSrinivasan, Madhusudhananen
kaust.authorLehväslaiho, Heikkien
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