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Technical autopsy of a custom biobank portal

Yves Sucaet, PhDDiabetes Research Center

CMI

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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