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Bringing Open Data to Whole Slide Imaging

  • Sébastien Besson
  • Roger Leigh
  • Melissa Linkert
  • Chris Allan
  • Jean-Marie Burel
  • Mark Carroll
  • David Gault
  • Riad Gozim
  • Simon Li
  • Dominik Lindner
  • Josh Moore
  • Will Moore
  • Petr Walczysko
  • Frances Wong
  • Jason R. SwedlowEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11435)

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.

Keywords

Whole slide imaging Open file format Open data OME-TIFF 

Notes

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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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Department of Computational Biology, School of Life SciencesUniversity of DundeeDundeeUK
  2. 2.Glencoe Software, Inc.SeattleUSA

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