The advent of

digital
microscopy
IT / ComS edition 

Yves Sucaet,
Wim Waelput,
Peter In’t Veld
Financial disclosure

• Yves Sucaet and Wim Waelput are co-founders and

shareholders in Pathomation, an innovative company founded
in 2012. The company strives to offer the most
comprehensive software platform for digital pathology
possible. The focus is on integration, scalability, and user-
friendliness. Pathomation implements digital pathology in a
variety of use cases and scenarios.

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Prelude

• In October 2016, I was honored at Troy University as one of

its 2016 “alumni of the year” during the annual homecoming
activities.
• In the following week, I gave several guest lectures in various
departments across campus.
• This is the lecture as presented for the Information Systems
(IT/ComS) department on Thursday, October 20, 2016.

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Topics for today

• How did I get here?

• Digital microscopy/pathology
• How does it work (technology)
• Big images, Big data, and deep learning

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PERSONAL BACKGROUND
 Who am I (education)?

Education
• 1998-2000: Hogeschool Gent (BE)
– BS Computer Sciences

• 2001-2005: Troy State University (US)

– Exchange program
• Developed an interest in using ComS to help (molecular) biologists
– MS Biological Sciences
• Research in yeast genetics with Dr. Christi Magrath (NSF fellowship)

• 2005-2010: Iowa State University

– PhD Bioinformatics & Computational Biology

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Who am I (professional)

Professional

• 2000-2001: Becton Dickinson

• 2010-2013: HistoGeneX
• Section head Data Management & Bioinformatics
• 2012-now: Pathomation
• Chief Technology Officer
• 2014-Q1 2017: VUB
• Digital Pathology Manager
• 2016-now: HistoGeneX
• Data scientist

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WHAT IS DIGITAL
MICROSCOPY/PATHOLOGY?
This is not a digital microscope

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Getting started with digital microscopy

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Whole slide imaging (single slide)

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Hardware

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Software stack

Very
large
image!

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How big are these images?

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Network topology at the VUB

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Confusing your end-users (customers)! NOT good!

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What’s the solution?

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Digital microscopy at the VUB

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What does the Pathomation software look like?

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Digital (r)evolution

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HOW DOES IT WORK?
How do the whole slide scanners work?

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Rendering HUGE image files (gigapixel)

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How much data are you transferring?

• It depends
• The original file is about 1GB
– But you only transfer data in packages of 512x512 px
– Optimize the speed of transfer by toggling the
compression ratio
• No impact on diagnostic accuracy!
– Tiles are downloaded in parallel
• Browser initiates 6 parallel downloads
– Tiles 7, 8, 9… are queued
• Optimize tile size for screen size
– Mobile devices vs. 4K screens

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So… how much data ARE you transferring?

• We wrote a profiler application

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Time taken to serve tiles

91.86% of the tiles were

Percent of content served

served below 200 ms,

including network time.

Time is milliseconds

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 And does it scale?
Number of tiles served within 10 minute timeframe

10 minute intervals

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Facilitating the European Society of Pathology

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BIG IMAGES, BIG DATA, AND DEEP
LEARNING
Once you have image data…

• Commercially • Free-of-charge, open

available source

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Pancreas analysis for diabetes research

Step 1: find tissue

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Pancreas analysis for diabetes research

Step 2: locate the islets

Step 1: find tissue

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Pancreas analysis for diabetes research

Step 3: quantitate insulin

Step 2: locate the islets

Step 1: find tissue

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More advanced: graph theory (Ackermann)

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More advanced: graph theory (Ackermann)

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More advanced: graph theory (Ackermann)

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More advanced: graph theory (Ackermann)

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But what does the graph mean (Ackermann)?

• Measured degree distributions show that:

– Cell positions are not random in the tissue
– CD30+ cells cluster in the tissue
– the cell graphs are not scale-free
• NextGen Sequencing, proteomics, microarrays etc…
– Are NOT the “answer to everything”
– Tissue is STILL the issue
• Topology matters!

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Deep learning as the new frontier (Van der Laak)

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Another way of looking at deep learning (Van der Laak)

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Do this for histology (Van der Laak)

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Does it work (Van der Laak)?

Pathologist HMS & MIT Radboudumc Exb METU

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Computational pathology as a decision support tool

Tumour
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IN CLOSING
Conclusions

• Digital pathology is ready for prime time

– Education and training,
– Research (including biobanking)
• DIY digital pathology
– Do your due diligence: hardware, software
• But even more important: ALGORITHMS
– DON’T spend all your resources on “stuff”
• Hire the right people to implement the right workflows
– All levels of IT expertise are needed!
– Start with one use case, expand to others
– Image analysis can significantly enhance the
profession of pathologists (wide open field!)
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Learn more about digital pathology

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Continue the conversation

• Email: yves.sucaet@gmail.com

Thank you for inviting me!

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