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Towards Better Digital Pathology Workflows:
Programming libraries for high-speedsharpness assessment of Whole Slide Images
David Ameisen - [email protected]
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Quality assessment in WSI:
a key step towards systematic use WSI scanners - FDA Class III Medical Devices :
13% of Whole Slide Images need to be scanned at least twice.Campbell WS et al., Human Path, 2012;
Concordance between whole-slide imaging and light microscopy for routine surgical pathology.
A posteriori visual quality verification is insufficient: partial verification.
Automatic Quality Assurance tools are not adapted to high dimensions (>10 9 pixels).
Our perspective: Make WSI Quality Assessment tools fast enough for any pathology workflow.
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7 years ofresearch in
WSIcollaborations
Quality
Assurance?
Major problem:
Blur
Research
Teaching
Clinical
Manual / Visual
Non-systematic
Non-quantified
Towards awidespread use
of WSI inpathology
Background
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State of the artCurrent methods and limits of automated image quality assurance
No Fast Blur Detection and Quantification
Solution for Whole Slide Images
Auto-focus One shot
Comparison Gold standard
No reference Too slow
Z-stack Too big
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Sharp; partially blurred; out of focus Absolute
Blur/SharpnessQuantification
Highly scalable, multi-core, multi-node
Compatibility: Windows, Mac OSX, Linux
No gold standard required
A Fast Blur Detection and QuantificationSolution for Whole Slide Images
3 billion pixels analyzed per minute on a recent computer(10 to 100 times faster than other methods)
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6
Whole Slide Imagechecked at all magnifications
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20x : 1.7 Billion pixels6589 tiles of 512x512px24% relevant tiles (non-blank)amon which 25% are
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Video : real-time
analysis
https://www.youtube.com/watch?v=eIunSx-a-ug
https://www.youtube.com/watch?v=eIunSx-a-ughttps://www.youtube.com/watch?v=eIunSx-a-ug8/11/2019 Automatic Quality Assessment of Whole Slide Images
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5000 images analyzed in our labInternet survey:
100 images, 7500+ answers
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Correlation algorithm/user votesImage classification into three groups:Out of focus, Partially blurred, Sharp
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DuringWSI
digitization
Applications :Saving time, increasing the quality
Identification and reacquisition of blurred tiles during thescanCertification of the WSIs general image quality
Just afterWSI
digitization
Reacquisition of the WSI with more suitable profiles
Notification sent to reacquire the WSI
ContinuousQuality
Assusrance
Notification sent to recalibrate the WSI acquisition system
WSI quality scoring integrated in the files metadata
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C++Library
ImplementationsScaling
Optimized, multi-core, multi-node
Highly scalable to match any throughput
APIsC++Java
Python
Embeddable in Whole Slide Image acquisition systems
Embeddable in Whole Slide Image management platforms
Embeddable in Whole Slide Image viewers
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Our references
Talk, 11th European Congress on Telepathology5th International Congress on Virtual Microscopy6-9 June 2012, Venice, Italy
Poster, Pathology Visions Conference ,October, 28-31, 2012, Baltimore, MA, USA.
Talk, 12th European Congress on Digital Pathology18-21 June 2014, Paris, France
FlexMIm - Projet R&D - 4 989 K Fonds Unique Interministriel n 142013-2015, Paris, France.
Talk, Pathology Visions Conference ,October, 20-21, 2014, San Francisco, CA, USA.
pre-seed funding
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Contact :
Laboratory : David Ameisen - [email protected] Idfinnov : Robert Marino [email protected]
mailto:[email protected]:[email protected]:[email protected]:[email protected]