Explaining "digital" in digital pathology
- 1. Explaining the “digital” in “digital pathology” Yves Sucaet January 2024 www.cytomine.com
- 3. If want the make the best tools…
- 4. … understand where data comes from
- 5. See also part 1
- 6. Innovations in hardware When papa data and mama data love each other very much… www.cytomine.com
- 7. From patient to (stained) slide(s)
- 8. From slide to pixels
- 9. From slide to pixels ???? And now something magical happens…
- 10. Historically speaking (late 19th century)
- 11. Biggest part of the 20th century
- 12. By the end of the 20th century
- 13. Beginning of the 21st century
- 14. More automation / robotization
- 15. Package it all into a single case
- 16. Now you have a slide scanner!
- 17. It’s still a microscope (exhibit C)
- 18. How do slide scanners work?
- 19. “Hey, what a great idea!”, says… everybody…
- 20. Many vendors = healthy market!
- 21. The software side of things
- 23. How big are these images? 20 GIGA pixel 14 MEGA pixel
- 24. Gigapixel images are pyramids
- 25. You can observe this effect in Cytomine
- 26. You can observe this effect in Cytomine
- 27. You can observe this effect in Cytomine
- 28. Serve the right tiles in real time = a tile server • “What is a tile server” video @ https://youtu.be/sepPIexKELE
- 30. Each came up with their own “format”
- 31. Existing solutions Open source and vendor-specific, standardization efforts
- 32. Own SDK • 3DHistech SlideAC • Philips iSyntax (older version?) • Hamamatsu ndpread.dll
- 33. First (universal) mover advantage: OpenSlide
- 35. OME-tiff
- 36. DICOM / WG26 / Supplement 145
- 38. The reality of file formats
- 39. The next (technical) frontier
- 40. Data in context
- 42. Talking points for future RND meetings • Cytomine native annotations • WKT format • Import / export modalities; documentation and use cases • Scalability demonstrators • Vendor-specific annotations • Embedded within .mrxs, .nd2, .vsi, .xml files • Third-party annotations • Visiopharm .mld file format • Indica labs .annotation (XML) file format • QuPath file format
- 43. Use cases
- 44. Use cases for digital pathology (from 30k feet) Application areas • Education EET • Research EER • Clinical / Pharma research EED • Clinical / Hospital EED Scenarios • Storage • Search • Sharing
- 45. The goal