Technical implementation details of a biobank portal enhanced with digital pathology features
-
Upload
yves-sucaet -
Category
Science
-
view
106 -
download
1
Transcript of Technical implementation details of a biobank portal enhanced with digital pathology features
![Page 1: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/1.jpg)
03-05-2023 pag. 1
Technical autopsy of a custom biobank portal
Yves Sucaet, PhDDiabetes Research Center
CMI
![Page 2: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/2.jpg)
03-05-2023 pag. 2
Financial disclosure
• I’m a co-founder and shareholder of Pathomation, a company mentioned in this presentation
![Page 3: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/3.jpg)
03-05-2023 pag. 3
The portal
Accessible via http://www.diabetesbiobank.org
![Page 4: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/4.jpg)
03-05-2023 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
![Page 5: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/5.jpg)
03-05-2023 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…
![Page 6: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/6.jpg)
03-05-2023 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?
![Page 7: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/7.jpg)
03-05-2023 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
![Page 8: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/8.jpg)
03-05-2023 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
![Page 9: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/9.jpg)
03-05-2023 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
![Page 10: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/10.jpg)
03-05-2023 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
![Page 11: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/11.jpg)
03-05-2023 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
![Page 12: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/12.jpg)
03-05-2023 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
![Page 13: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/13.jpg)
03-05-2023 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.coreUser management
File management
Slide set and collection
management
![Page 14: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/14.jpg)
03-05-2023 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.coreUser management
File management
Query collection
Authentication
![Page 15: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/15.jpg)
03-05-2023 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.coreUser management
File management
/thumbnail
Query collection
Authentication
![Page 16: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/16.jpg)
03-05-2023 pag. 16
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
![Page 17: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/17.jpg)
03-05-2023 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.coreUser management
File management
API
/thumbnail
Query collection
Authentication
![Page 18: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/18.jpg)
03-05-2023 pag. 18
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
![Page 19: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/19.jpg)
03-05-2023 pag. 19
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
![Page 20: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/20.jpg)
03-05-2023 pag. 20
Visitor statistics
![Page 21: Technical implementation details of a biobank portal enhanced with digital pathology features](https://reader036.fdocuments.net/reader036/viewer/2022070603/5870bd841a28ab0b4a8b6455/html5/thumbnails/21.jpg)
03-05-2023 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