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OpenSlide: A vendor-neutral software foundation for digital pathology.

Goode A, Gilbert B, Harkes J, Jukic D, Satyanarayanan M - J Pathol Inform (2013)

Bottom Line: This creates issues not only for pathologists, but also for interoperability.The library is extensible and easily interfaced to various programming languages.An application written to the OpenSlide interface can transparently handle multiple vendor formats.

View Article: PubMed Central - PubMed

Affiliation: School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States ; Google, Pittsburgh, PA, USA.

ABSTRACT
Although widely touted as a replacement for glass slides and microscopes in pathology, digital slides present major challenges in data storage, transmission, processing and interoperability. Since no universal data format is in widespread use for these images today, each vendor defines its own proprietary data formats, analysis tools, viewers and software libraries. This creates issues not only for pathologists, but also for interoperability. In this paper, we present the design and implementation of OpenSlide, a vendor-neutral C library for reading and manipulating digital slides of diverse vendor formats. The library is extensible and easily interfaced to various programming languages. An application written to the OpenSlide interface can transparently handle multiple vendor formats. OpenSlide is in use today by many academic and industrial organizations world-wide, including many research sites in the United States that are funded by the National Institutes of Health.

No MeSH data available.


Related in: MedlinePlus

How OpenSlide is used by PathFind
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Related In: Results  -  Collection

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Figure 3: How OpenSlide is used by PathFind

Mentions: As mentioned earlier, enabling knowledge from previously encountered entities to be brought to bear on an unknown, but similar-looking diagnostic entity is a valuable capability in pathology. Of course, “similar-looking” is expressed in terms of visual attributes that have specific significance to the pathology of the tissue sample being examined. PathFind is an OpenSlide-based tool that accepts a wide range of similarity-detection software called searchlets. Each searchlet is a plugin for the OpenDiamond® platform, which enables interactive, semi-automated, hypothesis-driven searches of complex images. (The OpenDiamond platform was created by the same research group that created OpenSlide.) For example, we have created searchlets for similarity detection of cytologic atypia and pagetoid spread in skin lesions, using a machine-learning technique called Semantic Texton Forests.[22] We have also created searchlets for attributes such as nuclear density using ImageJ,[23] an open-source tool supported by the National Institutes of Health. Figure 2 shows the user interface presented to a pathologist by PathFind. The pathologist can zoom and navigate case data just as he does with a microscope and glass slides today. At any point, he can request a search for archival digital slides that have areas similar to the area currently in view. The results that are returned include entire digital slides as well as specific matching regions within each of those digital slides. Figure 3 shows the end-to-end architecture of the whole system with the roles of OpenSlide and the OpenDiamond platform highlighted. For each result, associated metadata such as anonymized patient information and diagnosis are returned.


OpenSlide: A vendor-neutral software foundation for digital pathology.

Goode A, Gilbert B, Harkes J, Jukic D, Satyanarayanan M - J Pathol Inform (2013)

How OpenSlide is used by PathFind
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3815078&req=5

Figure 3: How OpenSlide is used by PathFind
Mentions: As mentioned earlier, enabling knowledge from previously encountered entities to be brought to bear on an unknown, but similar-looking diagnostic entity is a valuable capability in pathology. Of course, “similar-looking” is expressed in terms of visual attributes that have specific significance to the pathology of the tissue sample being examined. PathFind is an OpenSlide-based tool that accepts a wide range of similarity-detection software called searchlets. Each searchlet is a plugin for the OpenDiamond® platform, which enables interactive, semi-automated, hypothesis-driven searches of complex images. (The OpenDiamond platform was created by the same research group that created OpenSlide.) For example, we have created searchlets for similarity detection of cytologic atypia and pagetoid spread in skin lesions, using a machine-learning technique called Semantic Texton Forests.[22] We have also created searchlets for attributes such as nuclear density using ImageJ,[23] an open-source tool supported by the National Institutes of Health. Figure 2 shows the user interface presented to a pathologist by PathFind. The pathologist can zoom and navigate case data just as he does with a microscope and glass slides today. At any point, he can request a search for archival digital slides that have areas similar to the area currently in view. The results that are returned include entire digital slides as well as specific matching regions within each of those digital slides. Figure 3 shows the end-to-end architecture of the whole system with the roles of OpenSlide and the OpenDiamond platform highlighted. For each result, associated metadata such as anonymized patient information and diagnosis are returned.

Bottom Line: This creates issues not only for pathologists, but also for interoperability.The library is extensible and easily interfaced to various programming languages.An application written to the OpenSlide interface can transparently handle multiple vendor formats.

View Article: PubMed Central - PubMed

Affiliation: School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States ; Google, Pittsburgh, PA, USA.

ABSTRACT
Although widely touted as a replacement for glass slides and microscopes in pathology, digital slides present major challenges in data storage, transmission, processing and interoperability. Since no universal data format is in widespread use for these images today, each vendor defines its own proprietary data formats, analysis tools, viewers and software libraries. This creates issues not only for pathologists, but also for interoperability. In this paper, we present the design and implementation of OpenSlide, a vendor-neutral C library for reading and manipulating digital slides of diverse vendor formats. The library is extensible and easily interfaced to various programming languages. An application written to the OpenSlide interface can transparently handle multiple vendor formats. OpenSlide is in use today by many academic and industrial organizations world-wide, including many research sites in the United States that are funded by the National Institutes of Health.

No MeSH data available.


Related in: MedlinePlus