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02-05-2023 pag. 1
How digital pathology can add value to your biobank
Yves Sucaet, PhDDiabetes Research Center
CMI
02-05-2023 pag. 2
Who am I?
Education• 2000: Hogeschool Gent
(BE)– BS Computer Sciences
• 2001-2005: Troy State University (US)– Exchange program– MS Biological Sciences
• 2005-2010: Iowa State University– PhD Bioinformatics &
Computational Biology
Professional
• 2000-2001: Becton Dickinson
• 2010-2013: HistoGeneX• Data Management• Bioinformatics• Section head
• 2014-2016: VUB• Digital Pathology Manager
02-05-2023 pag. 3
Presentation outline
• Background– What is Whole Slide Imaging (WSI)– What is Digital Pathology
• What is a biobank?• Adding value to your biobank– By adding slide imaging data– By adding (semi)automated image analysis
• Things to consider
Innoviris portal introductieBackground
02-05-2023 pag. 5
What is Whole Slide Imaging (WSI)?
• The technique of converting glass-mounted microscopy material into a digital representation / image.
02-05-2023 pag. 6
Free University of Brussels setup
02-05-2023 pag. 7
Implementing WSI for end-users
Enhanced network infrastructure
I gave you slides; how do I get to
see these?We’ll send you a link that you can open with
your webbrowserCool!
02-05-2023 pag. 8
Am I doing digital pathology yet?
• Whole Slide Imaging– A technique– Get a scanner– Generate LOTS of data– Easy
• Digital (histo)pathology– A method, • a way of thinking
– Workflow management, integration
– USE the data • valorization
– Hard
02-05-2023 pag. 9
So you want to do digital pathology?
Education
Biobanking
Second opinion
Primary diagnosis
Research
QA
Start small; select one use case; implement it RIGHT; scale and build
on your success
Innoviris portal introductieWhat is a biobank?
02-05-2023 pag. 11
Why do we build biobanks?
– Show-case for patients and samples.
– Facilitates patient selection for studies.
– Permanent record of cases allows retrospective validation of studies.
02-05-2023 pag. 12
Flemish Biobank (CMI – BBMRI. vl)
• Minimal clinical data (OECD)• Extended epidemiological dataset• HLA, auto-immune data• Images
02-05-2023 pag. 13
Source material: slides and clinical data
Innoviris portal introductieAdding value to your biobank
02-05-2023 pag. 15
Opportunities for digital pathology
• Without digital histopathology: • With digital histopathology:
I’m looking for breast tumor tissue
Does the sample contain cancer cells
Is it in situ or invasive?
Is it hormone-responsive?
I’m looking for breast tumor tissue
Does the sample contain cancer cells
Is it in situ or invasive?
Is it hormone-responsive?
Sure; glad to help
Just trust us
Just trust us
We don’t have that information
Sure; glad to help
Have a look at the HE
Have a look at the HE and the immunostains (p63 – calponine)
Have a look at the immunostains and the fluo
data (FISH)
Fidelity increases, confident about requests, investments pay off
02-05-2023 pag. 16
Valorization through digital pathology
As you add more layers of data and move further down the pyramid, the value of the initial sample in the biobank increases and the biobank as a whole is likely to prove more useful.
02-05-2023 pag. 17
Step 1
02-05-2023 pag. 18
Step 1: adding imaging datahttp://histosrv.vub.ac.be/dbb
02-05-2023 pag. 19
Step 1: adding imaging datahttp://histosrv.vub.ac.be/dbb
02-05-2023 pag. 20
Step 1: adding imaging datahttp://histosrv.vub.ac.be/dbb
02-05-2023 pag. 21
Biobank “behind the scenes”
Custom ASP.net website http://histosrv.vub.ac.be/dbb
02-05-2023 pag. 22
Pathomation software architecture
Custom built
Public portal
02-05-2023 pag. 23
Step 2
02-05-2023 pag. 24
Step 2: image analysis
Step 1: find tissue
(Based on work by J. Watson, Pathology Visions meeting 2012)
02-05-2023 pag. 25
Step 2: image analysis
Step 1: find tissue
Step 2: locate the islets
(Based on work by J. Watson, Pathology Visions meeting 2012)
02-05-2023 pag. 26
Step 2: image analysis
Step 1: find tissue
Step 2: locate the islets
Step 3: quantitate insulin
(Based on work by J. Watson, Pathology Visions meeting 2012)
02-05-2023 pag. 27
The result: intelligent querying
I’m looking for pancreatic tissue from a patient with
recent onset diabetes and a susceptible HLA-DQ
genotype. At least y% of the islets still have to contain
insulin-producing cells
Here you go
Innoviris portal introductieThank you for taking the time to review these materialsContact me at [email protected] to continue the conversation
02-05-2023 pag. 29
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