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    Culling for Extreme-Scale Segmentation Volumes: A Hybrid Deterministic and Probabilistic Approach

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    08444102.pdf
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    Type
    Article
    Authors
    Beyer, Johanna
    Mohammed, Haneen cc
    Agus, Marco
    Al-Awami, Ali K. cc
    Pfister, Hanspeter
    Hadwiger, Markus cc
    KAUST Department
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Computer Science Program
    Visual Computing Center (VCC)
    KAUST Grant Number
    OSR-2015-CCF-2533-01
    Date
    2018-08-22
    Online Publication Date
    2018-08-22
    Print Publication Date
    2019-01
    Permanent link to this record
    http://hdl.handle.net/10754/630554
    
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    Abstract
    With the rapid increase in raw volume data sizes, such as terabyte-sized microscopy volumes, the corresponding segmentation label volumes have become extremely large as well. We focus on integer label data, whose efficient representation in memory, as well as fast random data access, pose an even greater challenge than the raw image data. Often, it is crucial to be able to rapidly identify which segments are located where, whether for empty space skipping for fast rendering, or for spatial proximity queries. We refer to this process as culling. In order to enable efficient culling of millions of labeled segments, we present a novel hybrid approach that combines deterministic and probabilistic representations of label data in a data-adaptive hierarchical data structure that we call the label list tree. In each node, we adaptively encode label data using either a probabilistic constant-time access representation for fast conservative culling, or a deterministic logarithmic-time access representation for exact queries. We choose the best data structures for representing the labels of each spatial region while building the label list tree. At run time, we further employ a novel query-adaptive culling strategy. While filtering a query down the tree, we prune it successively, and in each node adaptively select the representation that is best suited for evaluating the pruned query, depending on its size. We show an analysis of the efficiency of our approach with several large data sets from connectomics, including a brain scan with more than 13 million labeled segments, and compare our method to conventional culling approaches. Our approach achieves significant reductions in storage size as well as faster query times.
    Citation
    Beyer J, Mohammed H, Agus M, Al-Awami AK, Pfister H, et al. (2019) Culling for Extreme-Scale Segmentation Volumes: A Hybrid Deterministic and Probabilistic Approach. IEEE Transactions on Visualization and Computer Graphics 25: 1132–1141. Available: http://dx.doi.org/10.1109/TVCG.2018.2864847.
    Sponsors
    We thank John Keyser for the ‘KESM Mouse Brain’ data set [34]. This work is partially supported by King Abdullah University of Science and Technology (KAUST) and the KAUST Office of Sponsored Research (OSR) award OSR-2015-CCF-2533-01.
    Publisher
    Institute of Electrical and Electronics Engineers (IEEE)
    Journal
    IEEE Transactions on Visualization and Computer Graphics
    DOI
    10.1109/TVCG.2018.2864847
    Additional Links
    https://ieeexplore.ieee.org/document/8444102/
    ae974a485f413a2113503eed53cd6c53
    10.1109/TVCG.2018.2864847
    Scopus Count
    Collections
    Articles; Computer Science Program; Visual Computing Center (VCC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

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