technical implementation details of a biobank portal enhanced with digital pathology features
TRANSCRIPT
03-05-2023 pag. 1
Technical autopsy of a custom biobank portal
Yves Sucaet, PhDDiabetes Research Center
CMI
03-05-2023 pag. 2
Financial disclosure
• I’m a co-founder and shareholder of Pathomation, a company mentioned in this presentation
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The portal
Accessible via http://www.diabetesbiobank.org
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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
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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…
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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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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
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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
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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
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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
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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
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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
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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.coreUser management
File management
Slide set and collection
management
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Pathomation also generates thumbnails for
each slide
Integrated overview of available visuals
Biobank WSI repo
Set #1 Set #2 Set #3
API
/thumbnail
PMA.coreUser management
File management
Query collection
Authentication
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Pathomation is the guardian of case- and slide-
metadata
Metadata capture
Biobank WSI repo
Set #1 Set #2 Set #3
PMA.forms
API
PMA.coreUser management
File management
/thumbnail
Query collection
Authentication
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No limitations on user interface or design
Biobank WSI repo
Set #1 Set #2 Set #3
PMA.forms
PMA.coreUser management
File management
API
/thumbnail
Query collection
Authentication
Visualization and styling remain
under control of the custom portal
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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.coreUser management
File management
API
/thumbnail
Query collection
Authentication
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Seamless integration of WSI content
Biobank WSI repo
Set #1 Set #2 Set #3
PMA.zui viewport
PMA.forms
PMA.coreUser management
File management
API
/thumbnail
Query collection
Authentication
<div> integration
Slides and images can be embedded via an <iframe>
or via a <div> tag
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Biobank WSI repo
Set #1 Set #2 Set #3
A complete overview
PMA.zui viewport
PMA.forms
PMA.coreUser management
File management
API
/thumbnail
Query collection
Authentication
<div> integration
Pathomation makes sure that YOUR device
is supported, too
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Visitor statistics
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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