This is an exciting time to do microscopy with the development of digital tools. Recently, digital microscopy has centered around whole slide imaging (WSI), a term that refers to devices that can digitize (scan) an entire glass slide.
For healthcare, digital microscopy manifests itself in the pathology department (digital pathology): it is important to get the right case, to the right pathologist, at the right time, to make the right diagnosis. Digitizing data eliminates the boundaries of time and distance.
Digital microscopy can enhance efficiency and improve quality for various use cases, including teaching, research, as well as clinical settings.
2. 14-11-2016 pag. 2
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.
3. 14-11-2016 pag. 3
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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Who am I (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
Education
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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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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
Time is milliseconds
Percentofcontentserved
91.86% of the tiles were
served below 200 ms,
including network time.
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And does it scale?
Numberoftilesservedwithin10minutetimeframe
10 minute intervals
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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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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!)
