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    GPU-accelerated brain connectivity reconstruction and visualization in large-scale electron micrographs

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    Type
    Book Chapter
    Authors
    Jeong, Wonki
    Pfister, Hanspeter
    Beyer, Johanna
    Hadwiger, Markus cc
    KAUST Department
    Visual Computing Center (VCC)
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Computer Science Program
    Date
    2011
    Permanent link to this record
    http://hdl.handle.net/10754/575840
    
    Metadata
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    Abstract
    This chapter introduces a GPU-accelerated interactive, semiautomatic axon segmentation and visualization system. Two challenging problems have been addressed: the interactive 3D axon segmentation and the interactive 3D image filtering and rendering of implicit surfaces. The reconstruction of neural connections to understand the function of the brain is an emerging and active research area in neuroscience. With the advent of high-resolution scanning technologies, such as 3D light microscopy and electron microscopy (EM), reconstruction of complex 3D neural circuits from large volumes of neural tissues has become feasible. Among them, only EM data can provide sufficient resolution to identify synapses and to resolve extremely narrow neural processes. These high-resolution, large-scale datasets pose challenging problems, for example, how to process and manipulate large datasets to extract scientifically meaningful information using a compact representation in a reasonable processing time. The running time of the multiphase level set segmentation method has been measured on the CPU and GPU. The CPU version is implemented using the ITK image class and the ITK distance transform filter. The numerical part of the CPU implementation is similar to the GPU implementation for fair comparison. The main focus of this chapter is introducing the GPU algorithms and their implementation details, which are the core components of the interactive segmentation and visualization system. © 2011 Copyright © 2011 NVIDIA Corporation and Wen-mei W. Hwu Published by Elsevier Inc. All rights reserved..
    Citation
    Jeong, W.-K., Pfister, H., Beyer, J., & Hadwiger, M. (2011). GPU-Accelerated Brain Connectivity Reconstruction and Visualization in Large-Scale Electron Micrographs. GPU Computing Gems Emerald Edition, 793–812. doi:10.1016/b978-0-12-384988-5.00049-8
    Publisher
    Elsevier BV
    Journal
    GPU Computing Gems Emerald Edition
    ISBN
    9780123849885
    DOI
    10.1016/B978-0-12-384988-5.00049-8
    ae974a485f413a2113503eed53cd6c53
    10.1016/B978-0-12-384988-5.00049-8
    Scopus Count
    Collections
    Computer Science Program; Visual Computing Center (VCC); Book Chapters; Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division

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