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Technical implementation details of a biobank portal enhanced with digital pathology features

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Facilitating biobanks are a novel application for digital pathology. The Brussels Free University (VUB) and its teaching hospital UZ Brussel, together with the Belgian Diabetes Registry have developed one of the world’s largest biobanks in the domain of type 1 diabetes. The digital pathology platform of Pathomation was deployed to facilitate access to the tissue collection and promote basic and clinical research. Clinical data is available side by side to whole slide image data in a seamless and transparent interface, assisting the researcher to make an optimal selection of material of interest for a particular study. Digital pathology is thus presented as a natural add-on to a biobank query interface.

Technical implementation details of a biobank portal enhanced with digital pathology features

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Download to read offline
17-6-2016 pag. 1
Technical autopsy of a
custom biobank portal
Yves Sucaet, PhD
Diabetes Research Center
CMI
17-6-2016 pag. 2
Financial disclosure
• I’m a co-founder and shareholder of Pathomation, a company
mentioned in this presentation
17-6-2016 pag. 3
The portal
Accessible via http://www.diabetesbiobank.org
17-6-2016 pag. 4
Biobank Whole Slide Imaging (WSI)
repository of microscopy slides
Imagine that you want to offer access to external people
(researchers, physicians, pharma partners) access to your
biobank material
The beginning
17-6-2016 pag. 5
The data consists of different datasets: clinical data,
brightfield whole slide images, fluorescence snapshots
Biobank WSI repo
Set #1 Set #2 Set #3
Multiple collections, cases, slides…
17-6-2016 pag. 6
The cases to be included in the sets are contributed
from different sites throughout the organization
Biobank WSI repo
Set #1 Set #2 Set #3
Where do these slides come from anyway?

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Technical implementation details of a biobank portal enhanced with digital pathology features

  • 1. 17-6-2016 pag. 1 Technical autopsy of a custom biobank portal Yves Sucaet, PhD Diabetes Research Center CMI
  • 2. 17-6-2016 pag. 2 Financial disclosure • I’m a co-founder and shareholder of Pathomation, a company mentioned in this presentation
  • 3. 17-6-2016 pag. 3 The portal Accessible via http://www.diabetesbiobank.org
  • 4. 17-6-2016 pag. 4 Biobank Whole Slide Imaging (WSI) repository of microscopy slides Imagine that you want to offer access to external people (researchers, physicians, pharma partners) access to your biobank material The beginning
  • 5. 17-6-2016 pag. 5 The data consists of different datasets: clinical data, brightfield whole slide images, fluorescence snapshots Biobank WSI repo Set #1 Set #2 Set #3 Multiple collections, cases, slides…
  • 6. 17-6-2016 pag. 6 The cases to be included in the sets are contributed from different sites throughout the organization Biobank WSI repo Set #1 Set #2 Set #3 Where do these slides come from anyway?
  • 7. 17-6-2016 pag. 7 PMA.core Biobank WSI repo Set #1 Set #2 Set #3 Pathomation’s PMA.core central server makes it easy to manage all slides as a single dataset, regardless of their origin Abstraction layer for whole slide images
  • 8. 17-6-2016 pag. 8 PMA.core Biobank WSI repo Set #1 Set #2 Set #3 Authentication Pathomation’s PMA.core also allows for user authentication, tracking, and password management Beyond microscopic data abstraction
  • 9. 17-6-2016 pag. 9 Pathomation offers an API (Application Programming Interface) to allow interfacing with other application User management API PMA.core Biobank WSI repo Set #1 Set #2 Set #3 User management
  • 10. 17-6-2016 pag. 10 Authentication This means that a custom portal website, specifically built for a particular project, can use the user repository of Pathomation Single sign-on in the portal site Biobank WSI repo Set #1 Set #2 Set #3 API PMA.coreUser management
  • 11. 17-6-2016 pag. 11 A custom portal can still have its own workflow and access rules, built on top of Pathomation’s user repository Custom lists and formatting in the portal Biobank WSI repo Set #1 Set #2 Set #3 API Slide set and collection management Authentication PMA.coreUser management
  • 12. 17-6-2016 pag. 12 Query collection When the portal needs to know what cases are available, it asks Pathomation The portal can discover new cases automatically PMA.core Biobank WSI repo Set #1 Set #2 Set #3 API Slide set and collection management Authentication User management File management
  • 13. 17-6-2016 pag. 13 When the portal needs to know what slides are available in a case, it asks Pathomation Portal has custom search capabilities Biobank WSI repo Set #1 Set #2 Set #3 API Query collection Authentication PMA.core User management File management Slide set and collection management
  • 14. 17-6-2016 pag. 14 Pathomation also generates thumbnails for each slide Integrated overview of available visuals Biobank WSI repo Set #1 Set #2 Set #3 API /thumbnail PMA.core User management File management Query collection Authentication
  • 15. 17-6-2016 pag. 15 Pathomation is the guardian of case- and slide- metadata Metadata capture Biobank WSI repo Set #1 Set #2 Set #3 PMA.forms API PMA.core User management File management /thumbnail Query collection Authentication
  • 16. 17-6-2016 pag. 16 No limitations on user interface or design Biobank WSI repo Set #1 Set #2 Set #3 PMA.forms PMA.core User management File management API /thumbnail Query collection Authentication Visualization and styling remain under control of the custom portal
  • 17. 17-6-2016 pag. 17 No plugins required for viewing Biobank WSI repo PMA.zui viewport Set #1 Set #2 Set #3 Pathomation has a special component that allows slide viewing PMA.forms PMA.core User management File management API /thumbnail Query collection Authentication
  • 18. 17-6-2016 pag. 18 Seamless integration of WSI content Biobank WSI repo Set #1 Set #2 Set #3 PMA.zui viewport PMA.forms PMA.core User management File management API /thumbnail Query collection Authentication <div> integration Slides and images can be embedded via an <iframe> or via a <div> tag
  • 19. 17-6-2016 pag. 19 Biobank WSI repo Set #1 Set #2 Set #3 A complete overview PMA.zui viewport PMA.forms PMA.core User management File management API /thumbnail Query collection Authentication <div> integration Pathomation makes sure that YOUR device is supported, too
  • 21. 17-6-2016 pag. 21 Acknowledgements • Diabetes Research Center, VUB – Yves Sucaet – Silke Smeets – Stijn Piessens – Peter In’t Veld • Dept of Pathology, UZ Brussel – Wim Waelput – Ramses Forsyth CMI