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03-05-2023 pag. 1
Using digital pathology to enhance a biobank portal
Yves Sucaet, PhDDiabetes Research Center
03-05-2023 pag. 2
Financial disclosure
• I’m a co-founder and shareholder of Pathomation, one of the companies mentioned in this presentation
03-05-2023 pag. 3
Presentation outline
• Introduction: Whole Slide Imaging (WSI)• Current status of WSI at VUB
– Educational tools medical school– Biobank: retrospective histopathology collections – Biobank: prospective histopathology collections
• Future plans– Slide / Data Exchange Research and Clinics– Image analysis– Scaling
03-05-2023 pag. 4
What is Whole Slide Imaging (WSI)?
• The technique of converting glass-mounted microscopy material into a digital representation / image.
03-05-2023 pag. 5
Once you’re happy…
03-05-2023 pag. 6
VUB result (january 2015)
03-05-2023 pag. 7
Different imaging platforms
• BD Pathway– TIFF images, 12-or 16-bit per pixel, grayscale, non-pyramidical– Attovision software
• Zeiss– ZVI / CZI Images, multiple (fluorescent) channels– AxioVision Software / ZEN Studio
• Nikon– ND2 / TIFF images, multiple (fluorescent) channels– NIS Elements
• Leica / Aperio– SVS images, brightfield– Aperio eSlide Manager (formerly Spectrum)– Aperio ImageScope
• 3DHistech (UZBrussel)– MRXS, brightfield– Pannoramic Viewer
03-05-2023 pag. 8
Connecting equipment
Innoviris portal introductieTaking our first steps
Trying it out on volunteers (aka students)
03-05-2023 pag. 10
Use case 1: Education
03-05-2023 pag. 11
Use case 1: The first course
• Histology education at http://histology.vub.ac.be (GK, BMW)
03-05-2023 pag. 12
Use case 1: Additional course
• Pathology education at http://pathology.vub.ac.be (GK, BMW)
Innoviris portal introductieScaling up
Doing more than “just” education
03-05-2023 pag. 14
Use case 2: Retrospective collections
Pathologic Anatomy of the Pancreas in Juvenile Diabetes Mellitus (Diabetes 14:619, 1965).
Willy Gepts (1922-1991)
03-05-2023 pag. 15
Use case 2: archival slides and clinical data
03-05-2023 pag. 16
Use case 2: Retrospective collections
• Currently available: http://gepts.vub.ac.be
03-05-2023 pag. 17
Use case 2: International Collaboration
• http://foulis.vub.ac.be
03-05-2023 pag. 18
Use case 2: slide organization
03-05-2023 pag. 19
Use case 2: meta-data capturing
03-05-2023 pag. 20
Demo
• http://gepts.vub.ac.be • http://foulis.vub.ac.be
Innoviris portal introductiePutting our experience to good use
Digital pathology for the valorisation of a “live” biobank
03-05-2023 pag. 22
Use case 3: Biobank
– Show-case for patients and samples.
– Facilitates patient selection for studies.
– Permanent record of cases allows retrospective validation of studies.
03-05-2023 pag. 23
Vlaamse Biobank (CMI – BBMRI. vl)
• Minimal clinical data (OECD)• Extended epidemiological dataset• HLA, auto-immune data• Images
03-05-2023 pag. 24
Biobank problems
• 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
03-05-2023 pag. 25
Use case 3: Biobank (valorization)
03-05-2023 pag. 26
Use case 3: Biobank (inspiration)
03-05-2023 pag. 27
Use case 3: Our own biobank sitehttp://histosrv.vub.ac.be/dbb
03-05-2023 pag. 28
Use case 3: Biobank “behind the scenes”
Innoviris portal introductie
The VUB digital histopathology ecosystemMultiple imaging platforms, multiple users, multiple applications, multiple portal websites
03-05-2023 pag. 30
The future: Hospital and clinical
• Ongoing evaluation of scanner equipment– Currently 3DHistech on site
• Case presentation– “Easy” cases for medical school students (rotations)– Special cases (multidisciplinary oncology consults)– Residents in the pathology department
• Collection hosting– Historical (restrospective) collections
• Students, residents, hospital staff members (don’t need to be pathologists!)– Thesis support: collect data, evaluate
• in a uniform, centralized manner• Fielt study
– 200 cases, to be evaluated by different pathologists for tumor infiltrating immune cells, tumor cell %, PDL1 IHC staining evaluation in tumor and micro-environment
03-05-2023 pag. 31
The future: image analysis
Step 1: find tissue
Step 2: locate the islets
Step 3: quantitate insulin
03-05-2023 pag. 32
The future: 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
03-05-2023 pag. 33
A grassroot initiative
• Computational Pathology Workshop – CPW 2016
http://cpw.pathomation.com
03-05-2023 pag. 34
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