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

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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 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
CountryUnited Kingdom
CityWarwick
Period10/04/1913/04/19
Internet address

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Keywords

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

Cite this

Besson, S., Leigh, R., Linkert, M., Allan, C., Burel, J-M., Carroll, M., Gault, D., Gozim, R., Li, S., Lindner, D., Moore, J., Moore, W., Walczysko, P., Wong, F., & Swedlow, J. (2019). Bringing Open Data to Whole Slide Imaging. In C. C. Reyes-Aldasoro, A. Janowczyk, M. Veta, P. Bankhead, & K. Sirinukunwattana (Eds.), Digital Pathology: 15th European Congress, ECDP 2019, Warwick, UK, April 10–13, 2019, Proceedings (pp. 3-10). (Lecture Notes in Computer Science; Vol. 11435). Springer . https://doi.org/10.1007/978-3-030-23937-4_1