Abstractocyte: A Visual Tool for Exploring Nanoscale Astroglial Cells

Handle URI:
http://hdl.handle.net/10754/626428
Title:
Abstractocyte: A Visual Tool for Exploring Nanoscale Astroglial Cells
Authors:
Mohammed, Haneen ( 0000-0002-4535-1926 ) ; Al-Awami, Ali K. ( 0000-0002-8725-1958 ) ; Beyer, Johanna; Cali, Corrado; Magistretti, Pierre J. ( 0000-0002-6678-320X ) ; Pfister, Hanspeter; Hadwiger, Markus ( 0000-0003-1239-4871 )
Abstract:
This paper presents Abstractocyte, a system for the visual analysis of astrocytes and their relation to neurons, in nanoscale volumes of brain tissue. Astrocytes are glial cells, i.e., non-neuronal cells that support neurons and the nervous system. The study of astrocytes has immense potential for understanding brain function. However, their complex and widely-branching structure requires high-resolution electron microscopy imaging and makes visualization and analysis challenging. Furthermore, the structure and function of astrocytes is very different from neurons, and therefore requires the development of new visualization and analysis tools. With Abstractocyte, biologists can explore the morphology of astrocytes using various visual abstraction levels, while simultaneously analyzing neighboring neurons and their connectivity. We define a novel, conceptual 2D abstraction space for jointly visualizing astrocytes and neurons. Neuroscientists can choose a specific joint visualization as a point in this space. Interactively moving this point allows them to smoothly transition between different abstraction levels in an intuitive manner. In contrast to simply switching between different visualizations, this preserves the visual context and correlations throughout the transition. Users can smoothly navigate from concrete, highly-detailed 3D views to simplified and abstracted 2D views. In addition to investigating astrocytes, neurons, and their relationships, we enable the interactive analysis of the distribution of glycogen, which is of high importance to neuroscientists. We describe the design of Abstractocyte, and present three case studies in which neuroscientists have successfully used our system to assess astrocytic coverage of synapses, glycogen distribution in relation to synapses, and astrocytic-mitochondria coverage.
KAUST Department:
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Computer Science Program; Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program; Visual Computing Center (VCC)
Citation:
Mohammed H, Al-Awami AK, Beyer J, Cali C, Magistretti P, et al. (2018) Abstractocyte: A Visual Tool for Exploring Nanoscale Astroglial Cells. IEEE Transactions on Visualization and Computer Graphics 24: 853–861. Available: http://dx.doi.org/10.1109/TVCG.2017.2744278.
Publisher:
Institute of Electrical and Electronics Engineers (IEEE)
Journal:
IEEE Transactions on Visualization and Computer Graphics
KAUST Grant Number:
OSR-2015-CCF-2533-01
Issue Date:
28-Aug-2017
DOI:
10.1109/TVCG.2017.2744278
Type:
Article
ISSN:
1077-2626
Sponsors:
This work was supported by funding from King Abdullah University of Science and Technology (KAUST) and KAUST award OSR-2015-CCF-2533-01.
Additional Links:
http://ieeexplore.ieee.org/document/8017643/
Appears in Collections:
Articles; Bioscience Program; Computer Science Program; Visual Computing Center (VCC); Biological and Environmental Sciences and Engineering (BESE) Division; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorMohammed, Haneenen
dc.contributor.authorAl-Awami, Ali K.en
dc.contributor.authorBeyer, Johannaen
dc.contributor.authorCali, Corradoen
dc.contributor.authorMagistretti, Pierre J.en
dc.contributor.authorPfister, Hanspeteren
dc.contributor.authorHadwiger, Markusen
dc.date.accessioned2017-12-26T12:00:50Z-
dc.date.available2017-12-26T12:00:50Z-
dc.date.issued2017-08-28en
dc.identifier.citationMohammed H, Al-Awami AK, Beyer J, Cali C, Magistretti P, et al. (2018) Abstractocyte: A Visual Tool for Exploring Nanoscale Astroglial Cells. IEEE Transactions on Visualization and Computer Graphics 24: 853–861. Available: http://dx.doi.org/10.1109/TVCG.2017.2744278.en
dc.identifier.issn1077-2626en
dc.identifier.doi10.1109/TVCG.2017.2744278en
dc.identifier.urihttp://hdl.handle.net/10754/626428-
dc.description.abstractThis paper presents Abstractocyte, a system for the visual analysis of astrocytes and their relation to neurons, in nanoscale volumes of brain tissue. Astrocytes are glial cells, i.e., non-neuronal cells that support neurons and the nervous system. The study of astrocytes has immense potential for understanding brain function. However, their complex and widely-branching structure requires high-resolution electron microscopy imaging and makes visualization and analysis challenging. Furthermore, the structure and function of astrocytes is very different from neurons, and therefore requires the development of new visualization and analysis tools. With Abstractocyte, biologists can explore the morphology of astrocytes using various visual abstraction levels, while simultaneously analyzing neighboring neurons and their connectivity. We define a novel, conceptual 2D abstraction space for jointly visualizing astrocytes and neurons. Neuroscientists can choose a specific joint visualization as a point in this space. Interactively moving this point allows them to smoothly transition between different abstraction levels in an intuitive manner. In contrast to simply switching between different visualizations, this preserves the visual context and correlations throughout the transition. Users can smoothly navigate from concrete, highly-detailed 3D views to simplified and abstracted 2D views. In addition to investigating astrocytes, neurons, and their relationships, we enable the interactive analysis of the distribution of glycogen, which is of high importance to neuroscientists. We describe the design of Abstractocyte, and present three case studies in which neuroscientists have successfully used our system to assess astrocytic coverage of synapses, glycogen distribution in relation to synapses, and astrocytic-mitochondria coverage.en
dc.description.sponsorshipThis work was supported by funding from King Abdullah University of Science and Technology (KAUST) and KAUST award OSR-2015-CCF-2533-01.en
dc.publisherInstitute of Electrical and Electronics Engineers (IEEE)en
dc.relation.urlhttp://ieeexplore.ieee.org/document/8017643/en
dc.rights(c) 2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/ republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works.en
dc.subjectData visualizationen
dc.subjectNanoscale devicesen
dc.subjectNeuronsen
dc.subjectThree-dimensional displaysen
dc.subjectToolsen
dc.subjectTwo dimensional displaysen
dc.subjectVisualizationen
dc.titleAbstractocyte: A Visual Tool for Exploring Nanoscale Astroglial Cellsen
dc.typeArticleen
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentComputer Science Programen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentBioscience Programen
dc.contributor.departmentVisual Computing Center (VCC)en
dc.identifier.journalIEEE Transactions on Visualization and Computer Graphicsen
dc.eprint.versionPost-printen
dc.contributor.institutionJohn A. Paulson School of Engineering and Applied Sciences at Harvard University, Cambridge, MA, USAen
kaust.authorMohammed, Haneenen
kaust.authorAl-Awami, Ali K.en
kaust.authorCali, Corradoen
kaust.authorMagistretti, Pierre J.en
kaust.authorHadwiger, Markusen
kaust.grant.numberOSR-2015-CCF-2533-01-
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