Journal Article
. 2018 Dec; 9:37.
doi: 10.4103/jpi.jpi_42_18.

Implementing the DICOM Standard for Digital Pathology

Markus D Herrmann 1 David A Clunie 2 Andriy Fedorov 3 Sean W Doyle 1 Steven Pieper 4 Veronica Klepeis 5 Long P Le 5 George L Mutter 5 David S Milstone 5 Thomas J Schultz 6 Ron Kikinis 3 Gopal K Kotecha 1 David H Hwang 5 Katherine P Andriole 1 A John Iafrate 5 James A Brink 5 Giles W Boland 5 Keith J Dreyer 1 Mark Michalski 1 Jeffrey A Golden 5 David N Louis 5 Jochen K Lennerz 5 
Affiliations
  • PMID: 30533276
  •     35 References
  •     23 citations

Abstract

Background: Digital Imaging and Communications in Medicine (DICOM®) is the standard for the representation, storage, and communication of medical images and related information. A DICOM file format and communication protocol for pathology have been defined; however, adoption by vendors and in the field is pending. Here, we implemented the essential aspects of the standard and assessed its capabilities and limitations in a multisite, multivendor healthcare network.

Methods: We selected relevant DICOM attributes, developed a program that extracts pixel data and pixel-related metadata, integrated patient and specimen-related metadata, populated and encoded DICOM attributes, and stored DICOM files. We generated the files using image data from four vendor-specific image file formats and clinical metadata from two departments with different laboratory information systems. We validated the generated DICOM files using recognized DICOM validation tools and measured encoding, storage, and access efficiency for three image compression methods. Finally, we evaluated storing, querying, and retrieving data over the web using existing DICOM archive software.

Results: Whole slide image data can be encoded together with relevant patient and specimen-related metadata as DICOM objects. These objects can be accessed efficiently from files or through RESTful web services using existing software implementations. Performance measurements show that the choice of image compression method has a major impact on data access efficiency. For lossy compression, JPEG achieves the fastest compression/decompression rates. For lossless compression, JPEG-LS significantly outperforms JPEG 2000 with respect to data encoding and decoding speed.

Conclusion: Implementation of DICOM allows efficient access to image data as well as associated metadata. By leveraging a wealth of existing infrastructure solutions, the use of DICOM facilitates enterprise integration and data exchange for digital pathology.

Keywords: Computational pathology; DICOMweb; image compression; slide scanning; whole slide imaging.

Deep Learning Algorithms for Detection of Lymph Node Metastases From Breast Cancer: Helping Artificial Intelligence Be Seen.
Jeffrey Alan Golden.
JAMA, 2017 Dec 14; 318(22). PMID: 29234791
Computational Pathology: A Path Ahead.
David N Louis, Michael Feldman, +13 authors, Michael J Becich.
Arch Pathol Lab Med, 2015 Jun 23; 140(1). PMID: 26098131    Free PMC article.
A Foundation for Enterprise Imaging: HIMSS-SIIM Collaborative White Paper.
Christopher J Roth, Louis M Lannum, Kenneth R Persons.
J Digit Imaging, 2016 Jun 02; 29(5). PMID: 27245774    Free PMC article.
Review.
Enterprise Imaging Governance: HIMSS-SIIM Collaborative White Paper.
Christopher J Roth, Louis M Lannum, Carol L Joseph.
J Digit Imaging, 2016 Jun 16; 29(5). PMID: 27301709    Free PMC article.
Review.
DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research.
Andriy Fedorov, David Clunie, +9 authors, Reinhard R Beichel.
PeerJ, 2016 Jun 04; 4. PMID: 27257542    Free PMC article.
Standardizing the use of whole slide images in digital pathology.
Christel Daniel, Marcial García Rojo, +4 authors, Thomas Schrader.
Comput Med Imaging Graph, 2011 Jan 19; 35(7-8). PMID: 21242058
American Telemedicine Association clinical guidelines for telepathology.
Liron Pantanowitz, Kim Dickinson, +12 authors, Jordana Bernard.
J Pathol Inform, 2014 Nov 08; 5(1). PMID: 25379345    Free PMC article.
Implementation of whole slide imaging in surgical pathology: A value added approach.
Mike Isaacs, Jochen K Lennerz, +3 authors, John D Pfeifer.
J Pathol Inform, 2011 Oct 05; 2. PMID: 21969920    Free PMC article.
Integrating pathology and radiology disciplines: an emerging opportunity?
James Sorace, Denise R Aberle, +3 authors, W Dean Wallace.
BMC Med, 2012 Sep 07; 10. PMID: 22950414    Free PMC article.
Artificial Intelligence and the Pathologist: Future Frenemies?
Gaurav Sharma, Alexis Carter.
Arch Pathol Lab Med, 2017 Apr 28; 141(5). PMID: 28447905
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
Integrated Diagnostics: The Computational Revolution Catalyzing Cross-disciplinary Practices in Radiology, Pathology, and Genomics.
Claes F Lundström, Hannah L Gilmore, Pablo R Ros.
Radiology, 2017 Sep 20; 285(1). PMID: 28926318
Review.
Digital Imaging and Communications in Medicine Whole Slide Imaging Connectathon at Digital Pathology Association Pathology Visions 2017.
David Clunie, Dan Hosseinzadeh, +16 authors, Liron Pantanowitz.
J Pathol Inform, 2018 Apr 06; 9. PMID: 29619278    Free PMC article.
Introduction to the ACR-NEMA DICOM standard.
W D Bidgood, S C Horii.
Radiographics, 1992 Mar 11; 12(2). PMID: 1561424
Digital imaging standards and system interoperability.
U J Balis.
Clin Lab Med, 1997 Jun 01; 17(2). PMID: 9243076
ITK: enabling reproducible research and open science.
Matthew McCormick, Xiaoxiao Liu, +2 authors, Luis Ibanez.
Front Neuroinform, 2014 Mar 07; 8. PMID: 24600387    Free PMC article.
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.
Current State of the Regulatory Trajectory for Whole Slide Imaging Devices in the USA.
Esther Abels, Liron Pantanowitz.
J Pathol Inform, 2017 Jun 07; 8. PMID: 28584684    Free PMC article.
Review.
Overview of telepathology, virtual microscopy, and whole slide imaging: prospects for the future.
Ronald S Weinstein, Anna R Graham, +7 authors, John R Gilbertson.
Hum Pathol, 2009 Jun 26; 40(8). PMID: 19552937
1399 H&E-stained sentinel lymph node sections of breast cancer patients: the CAMELYON dataset.
Geert Litjens, Peter Bandi, +14 authors, Jeroen van der Laak.
Gigascience, 2018 Jun 04; 7(6). PMID: 29860392    Free PMC article.
Convolutional Deep Belief Network with Feature Encoding for Classification of Neuroblastoma Histological Images.
Soheila Gheisari, Daniel R Catchpoole, Amanda Charlton, Paul J Kennedy.
J Pathol Inform, 2018 Jun 05; 9. PMID: 29862127    Free PMC article.
Medical image file formats.
Michele Larobina, Loredana Murino.
J Digit Imaging, 2013 Dec 18; 27(2). PMID: 24338090    Free PMC article.
Review.
Technical Challenges of Enterprise Imaging: HIMSS-SIIM Collaborative White Paper.
David A Clunie, Don K Dennison, +3 authors, Henri Rik Primo.
J Digit Imaging, 2016 Sep 01; 29(5). PMID: 27576909    Free PMC article.
Review.
Whole Slide Imaging Versus Microscopy for Primary Diagnosis in Surgical Pathology: A Multicenter Blinded Randomized Noninferiority Study of 1992 Cases (Pivotal Study).
Sanjay Mukhopadhyay, Michael D Feldman, +31 authors, Clive R Taylor.
Am J Surg Pathol, 2017 Sep 30; 42(1). PMID: 28961557    Free PMC article.
The Orthanc Ecosystem for Medical Imaging.
Sébastien Jodogne.
J Digit Imaging, 2018 May 05; 31(3). PMID: 29725964    Free PMC article.
Review.
Straw Men, Deep Learning, and the Future of the Human Microscopist: Response to "Artificial Intelligence and the Pathologist: Future Frenemies?"
Scott R Granter, Andrew H Beck, David J Papke.
Arch Pathol Lab Med, 2017 Apr 28; 141(5). PMID: 28447901
The Design of SimpleITK.
Bradley C Lowekamp, David T Chen, Luis Ibáñez, Daniel Blezek.
Front Neuroinform, 2014 Jan 15; 7. PMID: 24416015    Free PMC article.
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.
Computational pathology: an emerging definition.
David N Louis, Georg K Gerber, +11 authors, Jeffrey A Golden.
Arch Pathol Lab Med, 2014 Aug 30; 138(9). PMID: 25171694
Machine Learning Compared With Pathologist Assessment.
Maarten van Smeden, Ben Van Calster, Rolf H H Groenwold.
JAMA, 2018 May 02; 319(16). PMID: 29710156
Digital pathology and anatomic pathology laboratory information system integration to support digital pathology sign-out.
Huazhang Guo, Joe Birsa, +9 authors, Liron Pantanowitz.
J Pathol Inform, 2016 May 25; 7. PMID: 27217973    Free PMC article.
Digital pathology: A systematic evaluation of the patent landscape.
Ioan C Cucoranu, Anil V Parwani, +2 authors, Liron Pantanowitz.
J Pathol Inform, 2014 Jul 25; 5(1). PMID: 25057430    Free PMC article.
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.
DICOMweb™: Background and Application of the Web Standard for Medical Imaging.
Brad W Genereaux, Donald K Dennison, +4 authors, Charles E Kahn.
J Digit Imaging, 2018 May 12; 31(3). PMID: 29748852    Free PMC article.
Review.
Using Free-Response Receiver Operating Characteristic Curves to Assess the Accuracy of Machine Diagnosis of Cancer.
Chaya S Moskowitz.
JAMA, 2017 Dec 14; 318(22). PMID: 29234793
Open access image repositories: high-quality data to enable machine learning research.
F Prior, J Almeida, +4 authors, J Saltz.
Clin Radiol, 2019 May 02; 75(1). PMID: 31040006    Free PMC article.
Computational pathology definitions, best practices, and recommendations for regulatory guidance: a white paper from the Digital Pathology Association.
Esther Abels, Liron Pantanowitz, +9 authors, Cleopatra Kozlowski.
J Pathol, 2019 Jul 30; 249(3). PMID: 31355445    Free PMC article.
Review.
Deep Learning for Whole Slide Image Analysis: An Overview.
Neofytos Dimitriou, Ognjen Arandjelović, Peter D Caie.
Front Med (Lausanne), 2019 Dec 12; 6. PMID: 31824952    Free PMC article.
Review.
Impact of JPEG 2000 compression on deep convolutional neural networks for metastatic cancer detection in histopathological images.
Farhad Ghazvinian Zanjani, Svitlana Zinger, +3 authors, Peter H N de With.
J Med Imaging (Bellingham), 2019 May 01; 6(2). PMID: 31037247    Free PMC article.
Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group.
Mohamed Amgad, Elisabeth Specht Stovgaard, +66 authors, International Immuno-Oncology Biomarker Working Group.
NPJ Breast Cancer, 2020 May 16; 6. PMID: 32411818    Free PMC article.
Review.
Open Health Imaging Foundation Viewer: An Extensible Open-Source Framework for Building Web-Based Imaging Applications to Support Cancer Research.
Erik Ziegler, Trinity Urban, +5 authors, Gordon J Harris.
JCO Clin Cancer Inform, 2020 Apr 24; 4. PMID: 32324447    Free PMC article.
Quantitative Imaging Informatics for Cancer Research.
Andrey Fedorov, Reinhard Beichel, +18 authors, Ron Kikinis.
JCO Clin Cancer Inform, 2020 May 12; 4. PMID: 32392097    Free PMC article.
Dual-Personality DICOM-TIFF for Whole Slide Images: A Migration Technique for Legacy Software.
David A Clunie.
J Pathol Inform, 2019 May 07; 10. PMID: 31057981    Free PMC article.
A Regulatory Science Initiative to Harmonize and Standardize Digital Pathology and Machine Learning Processes to Speed up Clinical Innovation to Patients.
Hetal Desai Marble, Richard Huang, +14 authors, Jochen K Lennerz.
J Pathol Inform, 2020 Oct 13; 11. PMID: 33042601    Free PMC article.
Display Characteristics and Their Impact on Digital Pathology: A Current Review of Pathologists' Future "Microscope".
Jacob T Abel, Peter Ouillette, +7 authors, David S McClintock.
J Pathol Inform, 2020 Oct 13; 11. PMID: 33042602    Free PMC article.
Review.
LibMI: An Open Source Library for Efficient Histopathological Image Processing.
Yuxin Dong, Pargorn Puttapirat, +2 authors, Chen Li.
J Pathol Inform, 2020 Oct 13; 11. PMID: 33042605    Free PMC article.
Reproducible Color Gamut of Hematoxylin and Eosin Stained Images in Standard Color Spaces.
Wei-Chung Cheng.
J Pathol Inform, 2020 Dec 22; 11. PMID: 33343996    Free PMC article.
[Technical, operational, and regulatory considerations for the adoption of digital and computational pathology].
Markus D Herrmann, Jochen K Lennerz.
Pathologe, 2020 Dec 03; 41(Suppl 2). PMID: 33263808
Review.

;. PMID: 33574288
Improved 3D U-Net robustness against JPEG 2000 compression for male pelvic organ segmentation in radiotherapy.
Karim El Khoury, Martin Fockedey, Eliott Brion, Benoît Macq.
J Med Imaging (Bellingham), 2021 Apr 13; 8(4). PMID: 33842669    Free PMC article.
Developing image analysis pipelines of whole-slide images: Pre- and post-processing.
Byron Smith, Meyke Hermsen, +2 authors, Walter Kremers.
J Clin Transl Sci, 2021 May 06; 5(1). PMID: 33948260    Free PMC article.
Review.
Artificial Intelligence in Pathology: From Prototype to Product.
André Homeyer, Johannes Lotz, +5 authors, Peter Hufnagl.
J Pathol Inform, 2021 May 21; 12. PMID: 34012717    Free PMC article.
Review.
Multispecialty Enterprise Imaging Workgroup Consensus on Interactive Multimedia Reporting Current State and Road to the Future: HIMSS-SIIM Collaborative White Paper.
Christopher J Roth, David A Clunie, +22 authors, Les R Folio.
J Digit Imaging, 2021 Jun 17; 34(3). PMID: 34131793    Free PMC article.
Review.
A review and guide to creating patient specific 3D printed anatomical models from MRI for benign gynecologic surgery.
Teresa E Flaxman, Carly M Cooke, +2 authors, Sukhbir S Singh.
3D Print Med, 2021 Jul 06; 7(1). PMID: 34224043    Free PMC article.
Review.
Dicom_wsi: A Python Implementation for Converting Whole-Slide Images to Digital Imaging and Communications in Medicine Compliant Files.
Qiangqiang Gu, Naresh Prodduturi, +2 authors, Steven N Hart.
J Pathol Inform, 2021 Jul 17; 12. PMID: 34267986    Free PMC article.
Tissue Multiplex Analyte Detection in Anatomic Pathology - Pathways to Clinical Implementation.
Keith A Wharton, Douglas Wood, +3 authors, Aleksandra Zuraw.
Front Mol Biosci, 2021 Aug 14; 8. PMID: 34386519    Free PMC article.
Review.
NCI Imaging Data Commons.
Andrey Fedorov, William J R Longabaugh, +25 authors, Ron Kikinis.
Cancer Res, 2021 Jun 30; 81(16). PMID: 34185678    Free PMC article.
Shifting Gears in Precision Oncology-Challenges and Opportunities of Integrative Data Analysis.
Ka-Won Noh, Reinhard Buettner, Sebastian Klein.
Biomolecules, 2021 Sep 29; 11(9). PMID: 34572523    Free PMC article.
Review.