25-05-2022 pag. 1 Prepared to scale: experiences with building a department-wide digital pathology infrastructure Yves Sucaet, PhD Diabetes Research Center
Jan 07, 2017
02-05-2023 pag. 1
Prepared to scale: experiences with building a department-wide digital
pathology infrastructureYves Sucaet, PhD
Diabetes Research Center
02-05-2023 pag. 2
Financial disclosure
• I’m a co-founder and shareholder of Pathomation, one of the companies mentioned in this presentation
02-05-2023 pag. 3
What is Whole Slide Imaging (WSI)?
• The technique of converting glass-mounted microscopy material into a digital representation / image.
02-05-2023 pag. 4
Why does it happen?
02-05-2023 pag. 5
Getting started in Brussels (january 2015)
02-05-2023 pag. 6
Once you’re happy…
02-05-2023 pag. 7
Infrastructure
02-05-2023 pag. 8
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
02-05-2023 pag. 9
Connecting equipment
Innoviris portal introductieTaking our first steps
Trying it out on volunteers (aka students)
02-05-2023 pag. 11
Use case 1: Education
02-05-2023 pag. 12
Use case 1: The first course
• Histology education at http://histology.vub.ac.be (GK, BMW)
02-05-2023 pag. 13
Use case 1: Additional course
• Pathology education at http://pathology.vub.ac.be (GK, BMW)
02-05-2023 pag. 14
Use case 1: Building on our success
02-05-2023 pag. 15
Use case 1: Going mobile
Innoviris portal introductieScaling up
Doing more than “just” education
http://www.diabetesbiobank.org
02-05-2023 pag. 17
Use case 2: Retrospective collections
Pathologic Anatomy of the Pancreas in Juvenile Diabetes Mellitus (Diabetes 14:619, 1965).
Willy Gepts (1922-1991)
02-05-2023 pag. 18
Use case 2: archival slides and clinical data
02-05-2023 pag. 19
Use case 2: Retrospective collections
• Currently available: http://gepts.vub.ac.be
02-05-2023 pag. 20
Use case 2: International Collaboration
• http://foulis.vub.ac.be
02-05-2023 pag. 21
Use case 2: slide organization
02-05-2023 pag. 22
Use case 2: meta-data capturing
Innoviris portal introductiePutting our experience to good use
Digital pathology for the valorisation of a “live” biobank
02-05-2023 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
02-05-2023 pag. 25
Use case 3: Our own biobank sitehttp://histosrv.vub.ac.be/dbb
02-05-2023 pag. 26
Use case 3: Biobank “behind the scenes”
Innoviris portal introductieThe future
02-05-2023 pag. 28
The future: image analysis
Step 1: find tissue
Step 2: locate the islets
Step 3: quantitate insulin
02-05-2023 pag. 29
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
02-05-2023 pag. 30
A grassroot initiative
• Computational Pathology Workshop – CPW 2016
http://cpw.pathomation.com
Innoviris portal introductieConclusions
02-05-2023 pag. 32
Publications
02-05-2023 pag. 33
Platform usage
02-05-2023 pag. 34
Software architecture enables users
02-05-2023 pag. 35
The VUB digital pathology ecosystem
Multiple imaging platforms, multiple users, multiple applications, multiple portal websites
02-05-2023 pag. 36
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