Large-scale storage of whole slide images and fast retrieval of tiles using DRAM

Daniel E. Lopez Barron; Praveen Rao; Deepthi Rao; Ossama Tawfik; Arun Zachariah

doi:10.1117/12.2564694

21 April 2020 Large-scale storage of whole slide images and fast retrieval of tiles using DRAM

Daniel E. Lopez Barron, Praveen Rao, Deepthi Rao, Ossama Tawfik, Arun Zachariah

Proceedings Volume 11395, Big Data II: Learning, Analytics, and Applications; 113950S (2020) https://doi.org/10.1117/12.2564694
Event: SPIE Defense + Commercial Sensing, 2020, Online Only

Abstract

The U.S. Food and Drug Administration (FDA) has approved two digital pathology systems for primary diagnosis. These systems produce and consume whole slide images (WSIs) constructed from glass slides using advanced digital slide scanners. WSIs can greatly improve the work ow of pathologists through the development of novel image analytics software for automatic detection of cellular and morphological features and disease diagnosis using histopathology slides. However, the gigabyte size of a WSI poses a serious challenge for storage and retrieval of millions of WSIs. In this paper, we propose a system for scalable storage of WSIs and fast retrieval of image tiles using DRAM. A WSI is partitioned into tiles and sub-tiles using a combination of a space-filling curve, recursive partitioning, and Dewey numbering. They are then stored as a collection of key-value pairs in DRAM. During retrieval, a tile is fetched using key-value lookups from DRAM. Through performance evaluation on a 24-node cluster using 100 WSIs, we observed that, compared to Apache Spark, our system was three times faster to store the 100 WSIs and 1,000 times faster to access a single tile achieving millisecond latency. Such fast access to tiles is highly desirable when developing deep learning-based image analytics solutions on millions of WSIs.

Conference Presentation

Citation Download Citation

Daniel E. Lopez Barron, Praveen Rao, Deepthi Rao, Ossama Tawfik, and Arun Zachariah "Large-scale storage of whole slide images and fast retrieval of tiles using DRAM", Proc. SPIE 11395, Big Data II: Learning, Analytics, and Applications, 113950S (21 April 2020); https://doi.org/10.1117/12.2564694

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