prepared to scale: experiences with building a department-wide digital pathology infrastructure
TRANSCRIPT
02-05-2023 pag. 1
Prepared to scale: experiences with building a department-wide digital
pathology infrastructureYves Sucaet, PhD
Diabetes Research Center
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Financial disclosure
• I’m a co-founder and shareholder of Pathomation, one of the companies mentioned in this presentation
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What is Whole Slide Imaging (WSI)?
• The technique of converting glass-mounted microscopy material into a digital representation / image.
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Why does it happen?
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Getting started in Brussels (january 2015)
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Once you’re happy…
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Infrastructure
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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
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Connecting equipment
Innoviris portal introductieTaking our first steps
Trying it out on volunteers (aka students)
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Use case 1: Education
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Use case 1: The first course
• Histology education at http://histology.vub.ac.be (GK, BMW)
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Use case 1: Additional course
• Pathology education at http://pathology.vub.ac.be (GK, BMW)
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Use case 1: Building on our success
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Use case 1: Going mobile
Innoviris portal introductieScaling up
Doing more than “just” education
http://www.diabetesbiobank.org
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Use case 2: Retrospective collections
Pathologic Anatomy of the Pancreas in Juvenile Diabetes Mellitus (Diabetes 14:619, 1965).
Willy Gepts (1922-1991)
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Use case 2: archival slides and clinical data
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Use case 2: Retrospective collections
• Currently available: http://gepts.vub.ac.be
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Use case 2: International Collaboration
• http://foulis.vub.ac.be
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Use case 2: slide organization
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Use case 2: meta-data capturing
Innoviris portal introductiePutting our experience to good use
Digital pathology for the valorisation of a “live” biobank
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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
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Use case 3: Our own biobank sitehttp://histosrv.vub.ac.be/dbb
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Use case 3: Biobank “behind the scenes”
Innoviris portal introductieThe future
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The future: image analysis
Step 1: find tissue
Step 2: locate the islets
Step 3: quantitate insulin
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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
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A grassroot initiative
• Computational Pathology Workshop – CPW 2016
http://cpw.pathomation.com
Innoviris portal introductieConclusions
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Publications
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Platform usage
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Software architecture enables users
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The VUB digital pathology ecosystem
Multiple imaging platforms, multiple users, multiple applications, multiple portal websites
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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
