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How to scale up and streamline your digital pathology operations with Mark Zarella



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You are already doing digital pathology in your institution but would like to scale it, take it to the next level? How do you do it, where do you start?

In this video my guest, Mark Zarella, PhD (previously Johns Hopkins University, currently Mayo Clinic) explains how he did exactly that at Johns Hopkins University.

He talks about:
- What is important when evaluating whole slide scanners and how to choose the best whole slide scanner for you
- How he organized and managed the whole slide images at Johns Hopkins University
- How he scaled the operations from ca. 10K slides to ca. 750K slides a year
- How he ensured interoperability of systems
- How he approached automated slide quality control

AND MUCH MUCH MORE!

If you are serious about taking your digital pathology operations to the next level, THIS IS THE EPISODE TO LISTEN TO!

//CHAPTERS
00:00 - 00:51 Introduction
00:52- Start of the podcast interview with Mark Zarella
1:28 - How did Mark start in Digital Pathology?
3:44 - Where are you now in your Digital Pathology Situation?
5:08 - How did you grow and in which direction?
6:35 - How much did the slide scanning capacity increase when you were at Johns Hopkins?
7:37 - What was the scanner selection journey?
7:49 - Paper: https://onlinelibrary.wiley.com/doi/epdf/10.1002/path.5923
8:00 - 3 primary considerations in scanner selection
9:10 - Which scanner do you evaluate in the paper and which one do you use?
11:56 - How do scanners from different vendors play together? How to make sure that they are interoperable?
14:13 - What was the worst thing to deal with when scaling the digital pathology operations? What was the biggest hurdle?
15:30 - What was your reason for keeping the images of different scanners separately?
17:00 - Automated quality control of whole slide images (Auto-QC)
18:34 - 3 things that Mark and his team looked at for Auto-QC
22:19 - Was the Auto QC done with classical image analysis or deep learning?
24:30 - How is Auto-QC integrated into the whole digital pathology workflow?
26:11 - What would be the number one piece of advice for those who want to start or scale digital pathology operations. What should they do, and what should they not do?
29:30 - How did you evaluate the already shortlisted scanners?
33:10 - Paper: https://onlinelibrary.wiley.com/doi/epdf/10.1002/path.5923
33:23 - Cool outro

THIS EPISODE'S RESOURCES

Mark's Paper: "High-throughput whole-slide scanning to enable large-scale data repository building" - https://onlinelibrary.wiley.com/doi/epdf/10.1002/path.5923

Blog post: HOW TO CHOOSE A WHOLE SLIDE IMAGING SCANNER FOR DIGITAL PATHOLOGY – THE ULTIMATE GUIDE - https://digitalpathologyplace.com/how-to-choose-a-whole-slide-imaging-scanner-for-digital-pathology-the-ultimate-guide/

Podcast episode: HOW TO CHOOSE A WHOLE SLIDE IMAGING SCANNER FOR DIGITAL PATHOLOGY W/ DOUG STAPLETON, HAMAMATSU - https://digitalpathologyplace.com/podcast/how-to-choose-a-digital-slide-scanner-w-doug-stapleton-hamamatsu/

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FREE RESOURCES FOR DIGITAL PATHOLOGY TRAILBLAZERS:

Digital Pathology Crash Course!
https://www.subscribepage.com/digital_pathology_crash_course

This is hands down the BEST place to start when it comes to digital pathology that will bring you up to speed or structure your current knowledge and launch your expertise. Don't miss it!

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NEXT TIER RESOURCES FOR DIGITAL PATHOLOGY TRAILBLAZERS:

Pathology 101 for non-pathologists
https://aleksandra-zuraw.mastermind.com/masterminds/27735

Are you starting your journey in tissue image analysis and computational pathology and are confused about what exactly you are supposed to analyze on the whole slide image?
I am finishing a course for computer scientists and professionals starting their journey in image analysis for pathology. This course will help you understand tissue and pathology without the necessity to deeply understand medicine. Join now!

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