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

doi:10.1007/978-3-030-23937-4_1

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 proceeding › Conference contribution

29 Citations (Scopus)

437 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 language	English
Title of host publication	Digital Pathology
Subtitle of host publication	15th European Congress, ECDP 2019, Warwick, UK, April 10–13, 2019, Proceedings
Editors	Constantino Carlos Reyes-Aldasoro, Andrew Janowczyk, Mitko Veta, Peter Bankhead, Korsuk Sirinukunwattana
Place of Publication	Switzerland
Publisher	Springer
Chapter	1
Pages	3-10
Number of pages	8
ISBN (Electronic)	9783030239374
ISBN (Print)	9783030239367
DOIs	https://doi.org/10.1007/978-3-030-23937-4_1
Publication status	Published - 2019
Event	15th European Congress on Digital Pathology (ECDP) - University of Warwick, Warwick, United Kingdom Duration: 10 Apr 2019 → 13 Apr 2019 Conference number: 15th https://www.ecdp2019.org/

Publication series

Name	Lecture Notes in Computer Science
Publisher	Springer
Volume	11435
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	15th European Congress on Digital Pathology (ECDP)
Abbreviated title	ECDP 2019
Country/Territory	United Kingdom
City	Warwick
Period	10/04/19 → 13/04/19
Internet address	https://www.ecdp2019.org/

Keywords

OME-TIFF
Open data
Open file format
Whole slide imaging

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-030-23937-4_1

Author Accepted Manuscript
This is a post-peer-review, pre-copyedit version of an article published in Digital Pathology: 15th European Congress, ECDP 2019, Warwick, UK, April 10–13, 2019, Proceedings. The final authenticated version is available online at: https://doi.org/10.1007/978-3-030-23937-4_1.
Accepted author manuscript, 1.16 MB

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

Besson, Sebastien ; Leigh, Roger ; Linkert, Melissa et al. / 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 ; Andrew Janowczyk ; Mitko Veta ; Peter Bankhead ; Korsuk Sirinukunwattana. Switzerland : Springer , 2019. pp. 3-10 (Lecture Notes in Computer Science).

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title = "Bringing Open Data to Whole Slide Imaging",

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.",

keywords = "OME-TIFF, Open data, Open file format, Whole slide imaging",

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",

note = "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).; 15th European Congress on Digital Pathology (ECDP), ECDP 2019 ; Conference date: 10-04-2019 Through 13-04-2019",

year = "2019",

doi = "10.1007/978-3-030-23937-4\_1",

language = "English",

isbn = "9783030239367",

series = "Lecture Notes in Computer Science",

publisher = "Springer ",

pages = "3--10",

editor = "Reyes-Aldasoro, \{Constantino Carlos\} and Andrew Janowczyk and Mitko Veta and Peter Bankhead and Korsuk Sirinukunwattana",

booktitle = "Digital Pathology",

url = "https://www.ecdp2019.org/",

}

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

Research output: Chapter in Book/Report/Conference proceeding › Conference 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 - Conference code: 15th

PY - 2019

Y1 - 2019

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.

KW - OME-TIFF

KW - Open data

KW - Open file format

KW - Whole slide imaging

UR - https://www.scopus.com/pages/publications/85069150747

U2 - 10.1007/978-3-030-23937-4_1

DO - 10.1007/978-3-030-23937-4_1

M3 - Conference contribution

C2 - 31579322

SN - 9783030239367

T3 - Lecture Notes in Computer Science

SP - 3

EP - 10

BT - Digital Pathology

A2 - Reyes-Aldasoro, Constantino Carlos

A2 - Janowczyk, Andrew

A2 - Veta, Mitko

A2 - Bankhead, Peter

A2 - Sirinukunwattana, Korsuk

PB - Springer

CY - Switzerland

T2 - 15th European Congress on Digital Pathology (ECDP)

Y2 - 10 April 2019 through 13 April 2019

ER -

Besson S, Leigh R, Linkert M, Allan C, Burel JM, Carroll M et al. Bringing Open Data to Whole Slide Imaging. In Reyes-Aldasoro CC, Janowczyk A, Veta M, 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). Epub 2019 Jul 3. doi: 10.1007/978-3-030-23937-4_1

Bringing Open Data to Whole Slide Imaging

Abstract

Publication series

Conference

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

BioStudies and the Image Data Resource: Expanding Imaging Datasets, Linkage, Metadata and Value (Joint with EMBL-EBI) (Bioinformatics and Biological Resources Fund - BBR)

New Open File Formats for the Biological Imaging Community

OME's Bio-Formats: Tools and Services for Data Access in Next-Generation Microscopy

Cite this

Bringing Open Data to Whole Slide Imaging

Abstract

Publication series

Conference

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Projects

BioStudies and the Image Data Resource: Expanding Imaging Datasets, Linkage, Metadata and Value (Joint with EMBL-EBI) (Bioinformatics and Biological Resources Fund - BBR)

New Open File Formats for the Biological Imaging Community

OME's Bio-Formats: Tools and Services for Data Access in Next-Generation Microscopy

Cite this