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Bringing Open Data to Whole Slide Imaging

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Book cover Digital Pathology (ECDP 2019)

Part of the book series: Lecture Notes in Computer Science ((LNIP,volume 11435))

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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 open-source library support for reading and writing pyramidal OME-TIFFs.

S. Besson, R. Leigh and M. Linkert—These authors contributed equally to this work.

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Acknowledgements

This work was funded by grants from the BBSRC (Ref: BB/P027032/1, BB/R015384/1) and the Wellcome Trust (Ref: 202908/Z/16/Z).

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Authors and Affiliations

  1. Department of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK

    Sébastien Besson, Roger Leigh, Jean-Marie Burel, Mark Carroll, David Gault, Riad Gozim, Simon Li, Dominik Lindner, Josh Moore, Will Moore, Petr Walczysko, Frances Wong & Jason R. Swedlow

  2. Glencoe Software, Inc., 800 5th Avenue, #101-259, Seattle, WA, 98104, USA

    Melissa Linkert, Chris Allan & Jason R. Swedlow

Authors
  1. Sébastien Besson
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  2. Roger Leigh
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  3. Melissa Linkert
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  4. Chris Allan
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  5. Jean-Marie Burel
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  6. Mark Carroll
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  7. David Gault
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  8. Riad Gozim
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  9. Simon Li
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  10. Dominik Lindner
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  11. Josh Moore
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  12. Will Moore
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  13. Petr Walczysko
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  14. Frances Wong
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  15. Jason R. Swedlow
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Corresponding author

Correspondence to Jason R. Swedlow .

Editor information

Editors and Affiliations

  1. Electrical Engineering, City, University of London, London, UK

    Constantino Carlos Reyes-Aldasoro

  2. Case Western Reserve University, Cleveland, OH, USA

    Andrew Janowczyk

  3. Eindhoven University of Technology, Eindhoven, The Netherlands

    Mitko Veta

  4. University of Edinburgh, Edinburgh, UK

    Peter Bankhead

  5. University of Oxford, Oxford, UK

    Korsuk Sirinukunwattana

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Besson, S. et al. (2019). Bringing Open Data to Whole Slide Imaging. In: Reyes-Aldasoro, C., Janowczyk, A., Veta, M., Bankhead, P., Sirinukunwattana, K. (eds) Digital Pathology. ECDP 2019. Lecture Notes in Computer Science(), vol 11435. Springer, Cham. https://doi.org/10.1007/978-3-030-23937-4_1

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  • DOI: https://doi.org/10.1007/978-3-030-23937-4_1

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-23936-7

  • Online ISBN: 978-3-030-23937-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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