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MaReIA: a cloud MapReduce based high performance whole slide image analysis framework

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Abstract

Recent advancements in systematic analysis of high resolution whole slide images have increase efficiency of diagnosis, prognosis and prediction of cancer and important diseases. Due to the enormous sizes and dimensions of whole slide images, the analysis requires extensive computing resources which are not commonly available. Images have to be tiled for processing due to computer memory limitations, which lead to inaccurate results due to the ignorance of boundary crossing objects. Thus, we propose a generic and highly scalable cloud-based image analysis framework for whole slide images. The framework enables parallelized integration of image analysis steps, such as segmentation and aggregation of micro-structures in a single pipeline, and generation of final objects manageable by databases. The core concept relies on the abstraction of objects in whole slide images as different classes of spatial geometries, which in turn can be handled as text based records in MapReduce. The framework applies an overlapping partitioning scheme on images, and provides parallelization of tiling and image segmentation based on MapReduce architecture. It further provides robust object normalization, graceful handling of boundary objects with an efficient spatial indexing based matching method to generate accurate results. Our experiments on Amazon EMR show that MaReIA is highly scalable, generic and extremely cost effective by benchmark tests.

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Notes

  1. https://tcga-data.nci.nih.gov/.

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Acknowledgements

This research is supported in part by Grants from National Science Foundation ACI 1443054 and IIS 1350885, National Institute of Health K25CA181503, and CNPq.

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Authors and Affiliations

  1. Department of Computer Science, Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA

    Hoang Vo, Yanhui Liang & Fusheng Wang

  2. Department of Biomedical Informatics, Emory University, Atlanta, GA, USA

    Jun Kong

  3. Department of Computer Science and Engineering, Ohio State University, Columbus, OH, USA

    Dejun Teng

  4. Hewlett Packard Labs, Palo Alto, CA, USA

    Ablimit Aji

  5. Department of Computer Science, University of Brasília, Brasília, DF, Brazil

    George Teodoro

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  1. Hoang Vo
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  2. Jun Kong
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  4. Yanhui Liang
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  5. Ablimit Aji
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  7. Fusheng Wang
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Correspondence to Hoang Vo.

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Vo, H., Kong, J., Teng, D. et al. MaReIA: a cloud MapReduce based high performance whole slide image analysis framework. Distrib Parallel Databases 37, 251–272 (2019). https://doi.org/10.1007/s10619-018-7237-1

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  • DOI: https://doi.org/10.1007/s10619-018-7237-1

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