Bringing Open Data to Whole Slide Imaging

Sebastien Besson, Roger Leigh, Melissa Linkert, Chris Allan, Jean-Marie Burel, Mark Carroll, David Gault, Riad Gozim, Simon Li, Dominik Lindner, Josh Moore, William Moore, Petr Walczysko, Frances Wong, Jason Swedlow (Lead / Corresponding author)

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    22 Citations (Scopus)
    308 Downloads (Pure)

    Abstract

    Faced with the need to support a growing number of whole slide imaging (WSI) file formats, our team has extended a long-standing community file format (OME-TIFF) for use in digital pathology. The format makes use of the core TIFF specification to store multi-resolution (or "pyramidal") representations of a single slide in a flexible, performant manner. Here we describe the structure of this format, its performance characteristics, as well as an opensource library support for reading and writing pyramidal OME-TIFFs.
    Original languageEnglish
    Title of host publicationDigital Pathology
    Subtitle of host publication15th European Congress, ECDP 2019, Warwick, UK, April 10–13, 2019, Proceedings
    EditorsConstantino Carlos Reyes-Aldasoro, Andrew Janowczyk, Mitko Veta, Peter Bankhead, Korsuk Sirinukunwattana
    Place of PublicationSwitzerland
    PublisherSpringer
    Chapter1
    Pages3-10
    Number of pages8
    ISBN (Electronic)9783030239374
    ISBN (Print)9783030239367
    DOIs
    Publication statusPublished - 2019
    Event15th European Congress on Digital Pathology (ECDP) - University of Warwick, Warwick, United Kingdom
    Duration: 10 Apr 201913 Apr 2019
    Conference number: 15th
    https://www.ecdp2019.org/

    Publication series

    NameLecture Notes in Computer Science
    PublisherSpringer
    Volume11435
    ISSN (Print)0302-9743
    ISSN (Electronic)1611-3349

    Conference

    Conference15th European Congress on Digital Pathology (ECDP)
    Abbreviated titleECDP 2019
    Country/TerritoryUnited Kingdom
    CityWarwick
    Period10/04/1913/04/19
    Internet address

    Keywords

    • OME-TIFF
    • Open data
    • Open file format
    • Whole slide imaging

    ASJC Scopus subject areas

    • Theoretical Computer Science
    • General Computer Science

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