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, Mitko Veta, Andrew Janowczyk, 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., ... Swedlow, J. (2019). Bringing Open Data to Whole Slide Imaging. In C. C. Reyes-Aldasoro, M. Veta, A. Janowczyk, 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). Switzerland: Springer . https://doi.org/10.1007/978-3-030-23937-4_1
Besson, Sebastien ; Leigh, Roger ; Linkert, Melissa ; Allan, Chris ; Burel, Jean-Marie ; Carroll, Mark ; Gault, David ; Gozim, Riad ; Li, Simon ; Lindner, Dominik ; Moore, Josh ; Moore, William ; Walczysko, Petr ; Wong, Frances ; Swedlow, Jason. / Bringing Open Data to Whole Slide Imaging. Digital Pathology: 15th European Congress, ECDP 2019, Warwick, UK, April 10–13, 2019, Proceedings. editor / Constantino Carlos Reyes-Aldasoro ; Mitko Veta ; Andrew Janowczyk ; Peter Bankhead ; Korsuk Sirinukunwattana. Switzerland : Springer , 2019. pp. 3-10 (Lecture Notes in Computer Science).
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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.",
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author = "Sebastien Besson and Roger Leigh and Melissa Linkert and Chris Allan and Jean-Marie Burel and Mark Carroll and David Gault and Riad Gozim and Simon Li and Dominik Lindner and Josh Moore and William Moore and Petr Walczysko and Frances Wong and Jason Swedlow",
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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 CC Reyes-Aldasoro, M Veta, A Janowczyk, P Bankhead & K Sirinukunwattana (eds), Digital Pathology: 15th European Congress, ECDP 2019, Warwick, UK, April 10–13, 2019, Proceedings. Lecture Notes in Computer Science, vol. 11435, Springer , Switzerland, pp. 3-10, 15th European Congress on Digital Pathology (ECDP), Warwick, United Kingdom, 10/04/19. https://doi.org/10.1007/978-3-030-23937-4_1

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

Digital Pathology: 15th European Congress, ECDP 2019, Warwick, UK, April 10–13, 2019, Proceedings. ed. / Constantino Carlos Reyes-Aldasoro; Mitko Veta; Andrew Janowczyk; Peter Bankhead; Korsuk Sirinukunwattana. Switzerland : Springer , 2019. p. 3-10 (Lecture Notes in Computer Science; Vol. 11435).

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

TY - GEN

T1 - Bringing Open Data to Whole Slide Imaging

AU - Besson, Sebastien

AU - Leigh, Roger

AU - Linkert, Melissa

AU - Allan, Chris

AU - Burel, Jean-Marie

AU - Carroll, Mark

AU - Gault, David

AU - Gozim, Riad

AU - Li, Simon

AU - Lindner, Dominik

AU - Moore, Josh

AU - Moore, William

AU - Walczysko, Petr

AU - Wong, Frances

AU - Swedlow, Jason

N1 - 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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N2 - 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.

AB - 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.

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M3 - Conference contribution

SN - 9783030239367

T3 - Lecture Notes in Computer Science

SP - 3

EP - 10

BT - Digital Pathology

A2 - Reyes-Aldasoro, Constantino Carlos

A2 - Veta, Mitko

A2 - Janowczyk, Andrew

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A2 - Sirinukunwattana, Korsuk

PB - Springer

CY - Switzerland

ER -

Besson S, Leigh R, Linkert M, Allan C, Burel J-M, Carroll M et al. Bringing Open Data to Whole Slide Imaging. In Reyes-Aldasoro CC, Veta M, Janowczyk A, Bankhead P, Sirinukunwattana K, editors, Digital Pathology: 15th European Congress, ECDP 2019, Warwick, UK, April 10–13, 2019, Proceedings. Switzerland: Springer . 2019. p. 3-10. (Lecture Notes in Computer Science). https://doi.org/10.1007/978-3-030-23937-4_1