Journal Article
. 2019 Oct; 2019:3-10.
doi: 10.1007/978-3-030-23937-4_1.

Bringing Open Data to Whole Slide Imaging

Sébastien Besson 1 Roger Leigh 1 Melissa Linkert 2 Chris Allan 2 Jean-Marie Burel 1 Mark Carroll 1 David Gault 1 Riad Gozim 1 Simon Li 1 Dominik Lindner 1 Josh Moore 1 Will Moore 1 Petr Walczysko 1 Frances Wong 1 Jason R Swedlow 1 
  • PMID: 31579322
  •     22 References
  •     4 citations


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: OME-TIFF; open data; open file format; whole slide imaging.

Metadata management for high content screening in OMERO.
Simon Li, Sébastien Besson, +18 authors, Jason R Swedlow.
Methods, 2015 Oct 18; 96. PMID: 26476368    Free PMC article.
The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging.
Ilya G Goldberg, Chris Allan, +7 authors, Jason R Swedlow.
Genome Biol, 2005 May 17; 6(5). PMID: 15892875    Free PMC article.
Proteomics. Tissue-based map of the human proteome.
Mathias Uhlén, Linn Fagerberg, +33 authors, Fredrik Pontén.
Science, 2015 Jan 24; 347(6220). PMID: 25613900
Highly Cited.
Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes.
Jia-Ren Lin, Benjamin Izar, +5 authors, Peter K Sorger.
Elife, 2018 Jul 12; 7. PMID: 29993362    Free PMC article.
Highly Cited.
Standardization in digital pathology: Supplement 145 of the DICOM standards.
Rajendra Singh, Lauren Chubb, Liron Pantanowitz, Anil Parwani.
J Pathol Inform, 2011 Jun 03; 2. PMID: 21633489    Free PMC article.
Perinodular and Intranodular Radiomic Features on Lung CT Images Distinguish Adenocarcinomas from Granulomas.
Niha Beig, Mohammadhadi Khorrami, +16 authors, Anant Madabhushi.
Radiology, 2018 Dec 19; 290(3). PMID: 30561278    Free PMC article.
Highly Cited.
OpenSlide: A vendor-neutral software foundation for digital pathology.
Adam Goode, Benjamin Gilbert, +2 authors, Mahadev Satyanarayanan.
J Pathol Inform, 2013 Nov 19; 4. PMID: 24244884    Free PMC article.
Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging.
Yury Goltsev, Nikolay Samusik, +5 authors, Garry P Nolan.
Cell, 2018 Aug 07; 174(4). PMID: 30078711    Free PMC article.
Highly Cited.
Diagnostic Assessment of Deep Learning Algorithms for Detection of Lymph Node Metastases in Women With Breast Cancer.
Babak Ehteshami Bejnordi, Mitko Veta, +67 authors, Rui Venâncio.
JAMA, 2017 Dec 14; 318(22). PMID: 29234806    Free PMC article.
Highly Cited.
The FAIR Guiding Principles for scientific data management and stewardship.
Mark D Wilkinson, Michel Dumontier, +50 authors, Barend Mons.
Sci Data, 2016 Mar 16; 3. PMID: 26978244    Free PMC article.
Highly Cited.
PD-L1 diagnostic tests: a systematic literature review of scoring algorithms and test-validation metrics.
Margarita Udall, Maria Rizzo, +4 authors, Eric Faulkner.
Diagn Pathol, 2018 Feb 11; 13(1). PMID: 29426340    Free PMC article.
Highly Cited. Systematic Review.
Glandular Morphometrics for Objective Grading of Colorectal Adenocarcinoma Histology Images.
Ruqayya Awan, Korsuk Sirinukunwattana, +6 authors, Nasir Rajpoot.
Sci Rep, 2017 Dec 06; 7(1). PMID: 29203775    Free PMC article.
Publishing and sharing multi-dimensional image data with OMERO.
Jean-Marie Burel, Sébastien Besson, +16 authors, Jason R Swedlow.
Mamm Genome, 2015 Aug 01; 26(9-10). PMID: 26223880    Free PMC article.
QuPath: Open source software for digital pathology image analysis.
Peter Bankhead, Maurice B Loughrey, +10 authors, Peter W Hamilton.
Sci Rep, 2017 Dec 06; 7(1). PMID: 29203879    Free PMC article.
Highly Cited.
An efficient architecture to support digital pathology in standard medical imaging repositories.
Tiago Marques Godinho, Rui Lebre, Luís Bastião Silva, Carlos Costa.
J Biomed Inform, 2017 Jun 13; 71. PMID: 28602907
The Image Data Resource: A Bioimage Data Integration and Publication Platform.
Eleanor Williams, Josh Moore, +10 authors, Jason R Swedlow.
Nat Methods, 2017 Aug 05; 14(8). PMID: 28775673    Free PMC article.
Highly Cited.
Novel digital signatures of tissue phenotypes for predicting distant metastasis in colorectal cancer.
Korsuk Sirinukunwattana, David Snead, +5 authors, Nasir Rajpoot.
Sci Rep, 2018 Sep 14; 8(1). PMID: 30209315    Free PMC article.
OMERO: flexible, model-driven data management for experimental biology.
Chris Allan, Jean-Marie Burel, +21 authors, Jason R Swedlow.
Nat Methods, 2012 Mar 01; 9(3). PMID: 22373911    Free PMC article.
Highly Cited.
EMPIAR: a public archive for raw electron microscopy image data.
Andrii Iudin, Paul K Korir, +2 authors, Ardan Patwardhan.
Nat Methods, 2016 Apr 14; 13(5). PMID: 27067018
Highly Cited.
Stable and discriminating features are predictive of cancer presence and Gleason grade in radical prostatectomy specimens: a multi-site study.
Patrick Leo, Robin Elliott, +3 authors, Anant Madabhushi.
Sci Rep, 2018 Oct 10; 8(1). PMID: 30297720    Free PMC article.
Deep learning for digital pathology image analysis: A comprehensive tutorial with selected use cases.
Andrew Janowczyk, Anant Madabhushi.
J Pathol Inform, 2016 Aug 27; 7. PMID: 27563488    Free PMC article.
Highly Cited.
Metadata matters: access to image data in the real world.
Melissa Linkert, Curtis T Rueden, +13 authors, Jason R Swedlow.
J Cell Biol, 2010 Jun 02; 189(5). PMID: 20513764    Free PMC article.
Highly Cited.
Open Practices and Resources for Collaborative Digital Pathology.
Raphaël Marée.
Front Med (Lausanne), 2019 Dec 05; 6. PMID: 31799253    Free PMC article.
TissUUmaps: interactive visualization of large-scale spatial gene expression and tissue morphology data.
Leslie Solorzano, Gabriele Partel, Carolina Wählby.
Bioinformatics, 2020 May 26; 36(15). PMID: 32449759    Free PMC article.
A Simple Method for Creating a High-Content Microscope for Imaging Multiplexed Tissue Microarrays.
Shabnam Abtahi, Neal R Gliksman, +7 authors, Jerrold R Turner.
Curr Protoc, 2021 Apr 07; 1(4). PMID: 33822482    Free PMC article.
Organ geometry channels reproductive cell fate in the Arabidopsis ovule primordium.
Elvira Hernandez-Lagana, Gabriella Mosca, +11 authors, Célia Baroux.
Elife, 2021 May 08; 10. PMID: 33960300    Free PMC article.