This document discusses the experiences of building a department-wide digital pathology infrastructure at the Vrije Universiteit Brussel. It began in January 2015 with whole slide imaging of glass slides on various platforms. This infrastructure was used for education through online histology and pathology courses. It also enabled retrospective studies of archived tissues by making slides available online along with associated clinical data. The digital platform has supported international collaboration and the development of a biobank site to provide virtual access to tissue samples. Future applications may include image analysis and intelligent querying of pathology images and associated metadata.

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Prepared to scale: experiences with
building a department-wide digital
pathology infrastructure
Yves 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

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• Taking 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

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• Scaling 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

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• Putting 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 site
http://histosrv.vub.ac.be/dbb

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Use case 3: Biobank “behind the scenes”

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• The 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

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• Conclusions

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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

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Questions?
• Email yves.sucaet@vub.ac.be