DICOM Format and Protocol Standardization—A Core Requirement for Digital Pathology Success

2020 ◽  
pp. 019262332096589
Author(s):  
David A. Clunie
Keyword(s):  
Digital Pathology ◽  
Virtual Microscopy ◽  
File Format ◽  
Whole Slide Imaging ◽  
Dicom Standard ◽  
Bright Field ◽  
Storage Security ◽  
Image File Format ◽  
Computational Pathology ◽  
Protocol Standardization

As the use of digital techniques in toxicologic pathology expands, challenges of scalability and interoperability come to the fore. Proprietary formats and closed single-vendor platforms prevail but depend on the availability and maintenance of multiformat conversion libraries. Expedient for small deployments, this is not sustainable at an industrial scale. Primarily known as a standard for radiology, the Digital Imaging and Communications in Medicine (DICOM) standard has been evolving to support other specialties since its inception, to become the single ubiquitous standard throughout medical imaging. The adoption of DICOM for whole slide imaging (WSI) has been sluggish. Prospects for widespread commercially viable clinical use of digital pathology change the incentives. Connectathons using DICOM have demonstrated its feasibility for WSI and virtual microscopy. Adoption of DICOM for digital and computational pathology will allow the reuse of enterprise-wide infrastructure for storage, security, and business continuity. The DICOM embedded metadata allows detached files to remain useful. Bright-field and multichannel fluorescence, Z-stacks, cytology, and sparse and fully tiled encoding are supported. External terminologies and standard compression schemes are supported. Color consistency is defined using International Color Consortium profiles. The DICOM files can be dual personality Tagged Image File Format (TIFF) for legacy support. Annotations for computational pathology results can be encoded.

Dawn of artificial intelligence -Enable digital Pathology in Pakistan-A paradigm shift

2021 ◽  
pp. 1-5
Author(s):  
Talat Zehra ◽  
Asma Shaikh ◽  
Maheen Shams
Keyword(s):  
Artificial Intelligence ◽  
Data Storage ◽  
Digital Pathology ◽  
Whole Slide Imaging ◽  
Storage Devices ◽  
New Horizons ◽  
Novel Technology ◽  
The World ◽  
Slide Image ◽  
Computational Pathology

Pathology particularly histopathology is considered to be a busy and challenging field. It is considered as gold standard for the diagnosis and management of patient particularly in cases of tumor. It has been more than twenty years since the introduction of whole slide imaging (WSI) in the developed part of the world. Various whole slide image (WSI) devices and use of artificial intelligence (AI) based softwares have transformed the field of Pathology1. Digital pathology is a novel technology and currently being implemented in most of the developed part of the world.2 Once the patient’s data becomes digital, it is easily stored, reproducible on a single click and quality remains same. This data can be used to make disease models, disease trends and predict the outcome of a particular disease through data mining which will open new horizons of precise medicine. The use of WSI with computational pathology and data storage devices have revolutionized the working in histopathology. The world witnessed an exponential rise in its adoption particularly after Covid-19 pandemic1. However, in the developing world either it is not being implemented or its use is still sub-optimal. By realizing the potential of digital and computational pathology along with the use of artificial intelligence software, we can bring a drastic change in the field of personalized medicine in the developing part of the world 3. Numerous validation studies have been published indicating that WSI is a reliable tool for routine diagnosis in surgical pathology 4   Continuous...

Evaluating whole-slide imaging viewers used in digital pathology

2020 ◽  
Vol 2020 (9) ◽  
pp. 372-1-372-6
Author(s):  
Wei-Chung Cheng ◽  
Samuel Lam ◽  
Qi Gong ◽  
Paul Lemaillet
Keyword(s):  
Digital Pathology ◽  
Software Tool ◽  
Color Difference ◽  
Third Party ◽  
File Format ◽  
Whole Slide Imaging ◽  
The Past ◽  
Compressed Images ◽  
File Formats ◽  
Color Differences

As a Class II medical device, whole-slide imaging (WSI) systems are emerging to succeed light microscopes used by pathologists in the past decades by digitalizing histological tissue slides into millions of pixels saved in a WSI file. Unlike the standard image file formats such as JPEG or TIFF, a WSI file usually consists of hundreds of compressed images of different magnification levels and focal planes that need to be decompressed, stitched, scaled, and colormanaged to reproduce the view demanded by the user with zooming and panning operations. Currently, most WSI files are stored in proprietary file formats, due to the lack of adopting a standard WSI file format, which hinders the development of third-party WSI viewers by making it difficult to interpret WSI files faithfully. To examine the fidelity of third-party WSI viewers, in this study, three freely available viewers, Sedeen, QuPath, and ASAP, were compared with the factory viewer, NDP, at the pixel level. A software tool was developed to register and calculate the 1976 CIE color difference for each pixel between two viewers. The average color differences were found as 1.30, 18.69, and 18.79 ΔE for Sedeen, QuPath, and ASAP, respectively.

scholarly journals Integrated Pathology Informatics Enables High-Quality Personalized and Precision Medicine: Digital Pathology and Beyond

2017 ◽  
Vol 142 (3) ◽  
pp. 369-382 ◽  
Author(s):  
Zoya Volynskaya ◽  
Hung Chow ◽  
Andrew Evans ◽  
Alan Wolff ◽  
Cecilia Lagmay-Traya; ◽  
...  
Keyword(s):  
Data Collection ◽  
Precision Medicine ◽  
Critical Role ◽  
Digital Pathology ◽  
Geographic Area ◽  
Whole Slide Imaging ◽  
High Quality ◽  
Pathology Informatics ◽  
Prognosis And Prediction ◽  
The Right

Context.— The critical role of pathology in diagnosis, prognosis, and prediction demands high-quality subspecialty diagnostics that integrates information from multiple laboratories. Objective.— To identify key requirements and to establish a systematic approach to providing high-quality pathology in a health care system that is responsible for services across a large geographic area. Design.— This report focuses on the development of a multisite pathology informatics platform to support high-quality surgical pathology and hematopathology using a sophisticated laboratory information system and whole slide imaging for histology and immunohistochemistry, integrated with ancillary tools, including electron microscopy, flow cytometry, cytogenetics, and molecular diagnostics. Results.— These tools enable patients in numerous geographic locations access to a model of subspecialty pathology that allows reporting of every specimen by the right pathologist at the right time. The use of whole slide imaging for multidisciplinary case conferences enables better communication among members of patient care teams. The system encourages data collection using a discrete data synoptic reporting module, has implemented documentation of quality assurance activities, and allows workload measurement, providing examples of additional benefits that can be gained by this electronic approach to pathology. Conclusion.— This approach builds the foundation for accurate big data collection and high-quality personalized and precision medicine.

scholarly journals A Practical Guide to Whole Slide Imaging: A White Paper From the Digital Pathology Association

2018 ◽  
Vol 143 (2) ◽  
pp. 222-234 ◽  
Author(s):  
Mark D. Zarella ◽  
Douglas Bowman; ◽  
Famke Aeffner ◽  
Navid Farahani ◽  
Albert Xthona; ◽  
...  
Keyword(s):  
Practical Knowledge ◽  
Digital Pathology ◽  
Executive Leadership ◽  
The United States ◽  
White Paper ◽  
Primary Diagnosis ◽  
Basic Function ◽  
Whole Slide Imaging ◽  
Interinstitutional Collaboration ◽  
Glass Slides

Context.— Whole slide imaging (WSI) represents a paradigm shift in pathology, serving as a necessary first step for a wide array of digital tools to enter the field. Its basic function is to digitize glass slides, but its impact on pathology workflows, reproducibility, dissemination of educational material, expansion of service to underprivileged areas, and intrainstitutional and interinstitutional collaboration exemplifies a significant innovative movement with far-reaching effects. Although the benefits of WSI to pathology practices, academic centers, and research institutions are many, the complexities of implementation remain an obstacle to widespread adoption. In the wake of the first regulatory clearance of WSI for primary diagnosis in the United States, some barriers to adoption have fallen. Nevertheless, implementation of WSI remains a difficult prospect for many institutions, especially those with stakeholders unfamiliar with the technologies necessary to implement a system or who cannot effectively communicate to executive leadership and sponsors the benefits of a technology that may lack clear and immediate reimbursement opportunity. Objectives.— To present an overview of WSI technology—present and future—and to demonstrate several immediate applications of WSI that support pathology practice, medical education, research, and collaboration. Data Sources.— Peer-reviewed literature was reviewed by pathologists, scientists, and technologists who have practical knowledge of and experience with WSI. Conclusions.— Implementation of WSI is a multifaceted and inherently multidisciplinary endeavor requiring contributions from pathologists, technologists, and executive leadership. Improved understanding of the current challenges to implementation, as well as the benefits and successes of the technology, can help prospective users identify the best path for success.

scholarly journals Update on the current opinion, status and future development of digital pathology in Switzerland in light of COVID-19

2021 ◽  
pp. jclinpath-2021-207768
Author(s):  
Viktor Hendrik Koelzer ◽  
Rainer Grobholz ◽  
Inti Zlobec ◽  
Andrew Janowczyk
Keyword(s):  
Early Stage ◽  
Digital Pathology ◽  
Primary Diagnosis ◽  
Imaging Systems ◽  
Whole Slide Imaging ◽  
University Hospitals ◽  
Primary Diagnostics ◽  
Personal Experiences ◽  
Standard Operating ◽  
Analogue To Digital

AimsThe transition from analogue to digital pathology (DP) in Switzerland has coincided with the COVID-19 crisis. The Swiss Digital Pathology Consortium conducted a national survey to assess the experience of pathologists in dealing with the challenges of the pandemic and how this has influenced the outlook and adoption of DP.MethodsA survey containing 20 questions relating to DP, personal experiences and challenges during the pandemic was addressed to Swiss pathologists at different experience stages in private practice, community and university hospitals.ResultsAll 74 respondents were pathologists, with 81.1% reporting more than 5 years of diagnostic service experience. 32.5% reported having read 100 digital slides or more in a diagnostic context. 39.2% reported using whole slide imaging systems at their primary workplace. Key DP use cases before the COVID-19 lockdown were tumour boards (39.2%), education (60.8%) and research (44.6%), with DP used for primary diagnosis in 13.5%. During the COVID-19 crisis, the use of DP for primary diagnostics more than doubled (30% vs 13.5%), with internal consults as important drivers (22.5% vs 16.5%), while research use (25% vs 44.6%) and external consults (17.5% vs 41.9%) strongly decreased. Key challenges identified included a lack of established standard operating procedures and availability of specialised hardware and software.ConclusionsThis survey indicates that the crisis acted as a catalyst in promoting DP adoption in centres where basic workflows were already established while posing major technical and organisational challenges in institutions that were at an early stage of DP implementation.

scholarly journals Digital Imaging and Communications in Medicine Whole Slide Imaging Connectathon at Digital Pathology Association Pathology Visions 2017

2018 ◽  
Vol 9 (1) ◽  
pp. 6 ◽  
Author(s):  
Liron Pantanowitz ◽  
David Clunie ◽  
Dan Hosseinzadeh ◽  
Mikael Wintell ◽  
David De Mena ◽  
...  
Keyword(s):  
Digital Imaging ◽  
Digital Pathology ◽  
Whole Slide Imaging

Digital Pathology and Virtual Microscopy Integration in E-Health Records

2010 ◽  
pp. 457-484 ◽  
Author(s):  
Marcial García Rojo ◽  
Christel Daniel
Keyword(s):  
Biomedical Research ◽  
Digital Pathology ◽  
Virtual Microscopy ◽  
Limiting Factors ◽  
Snomed Ct ◽  
Health Records ◽  
Anatomic Pathology ◽  
Healthcare Enterprise ◽  
Information Management Systems ◽  
Research And Education

In anatomic pathology, digital pathology integrates information management systems to manage both digital images and text-based information. Digital pathology allows information sharing for diagnosis, biomedical research and education. Virtual microscopy resulting in digital slides is an outreaching technology in anatomic pathology. Limiting factors in the expansion of virtual microscopy are formidable storage dimension, scanning speed, quality of image and cultural change. Anatomic pathology data and images should be an important part of the patient electronic health records as well as of clinical datawarehouses, epidemiological or biomedical research databases, and platforms dedicated to translational medicine. Integrating anatomic pathology to the “healthcare enterprise” can only be achieved using existing and emerging medical informatics standards like Digital Imaging and Communications in Medicine (DICOM®1), Health Level Seven (HL7®), and Systematized Nomenclature of Medicine-Clinical Terms (SNOMED CT®), following the recommendations of Integrating the Healthcare Enterprise (IHE®).

scholarly journals Toxicologic Pathology Forum*: Opinion on Integrating Innovative Digital Pathology Tools in the Regulatory Framework

2019 ◽  
Vol 47 (4) ◽  
pp. 436-443 ◽  
Author(s):  
Béatrice E. Gauthier ◽  
Frédéric Gervais ◽  
Gregory Hamm ◽  
Donal O’Shea ◽  
Alain Piton ◽  
...  
Keyword(s):  
Digital Pathology ◽  
Whole Slide Imaging ◽  
Software Validation ◽  
French Society ◽  
Laboratory Practice ◽  
Qualitative And Quantitative ◽  
Annual Congress ◽  
Good Laboratory ◽  
Practice Framework ◽  
Opinion Article

Digital pathology is defined as the ability to examine digitized microscopic slides and to generate qualitative and quantitative data. The field of digital pathology is rapidly evolving and has the potential to revolutionize toxicologic pathology. Techniques such as automated 2-D image analysis, whole slide imaging, and telepathology are already considered “mature” technologies and have been used for decades in exploratory studies; however, many organizations are reluctant to use digital pathology in regulatory toxicology studies. Innovative technologies using digitized slides including high-content imaging modalities and artificial intelligence are still under development but are increasingly used in toxicologic pathology. While software validation requirements are already described, clear guidance for application of these rules to the digital pathology field are few and the acceptance of these technologies by regulatory authorities remains necessary for successful adoption of digital pathology into the mainstream of toxicologic pathology. This topic was discussed during a roundtable at the 2018 Annual Congress of the French Society of Toxicologic Pathology. This opinion article summarizes the discussion regarding the current questions and challenges on the integration of innovative digital pathology tools within a good laboratory practice framework and is meant to stimulate further discussion among the toxicologic pathology community. [Box: see text]

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