Towards Better Digital Pathology Workflows:

Programming libraries for high-speed

sharpness assessment of Whole Slide Images
David Ameisen - david.ameisen@gmail.com
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.
7 years of
research in
WSI
collaborations
Quality
Assurance
?
Major problem:
Blur
Research
Teaching
Clinical
Manual / Visual
Non-systematic
Non-quantified
Towards a
widespread use
of WSI in
pathology
Background
State of the art
Current 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
Sharp; partially blurred; out of focus
Absolute
Blur/Sharpness
Quantification
Highly scalable, multi-core, multi-node
Compatibility: Windows, Mac OSX, Linux
No gold standard required
A Fast Blur Detection and Quantification
Solution for Whole Slide Images
3 billion pixels analyzed per minute on a recent computer
(10 to 100 times faster than other methods)
6
Whole Slide Image
checked at all magnifications
20x : 1.7 Billion pixels
6589 tiles of 512x512px
24% relevant tiles (non-
blank)
among which 25% are
sharp
34 seconds on a 2012
laptop
Video : real-time
analysis
https://www.youtube.com/watch?v=eIunSx-a-ug
5000 images analyzed in our lab
Internet survey:
100 images, 7500+ answers
Correlation algorithm/user votes
Image classification into three groups:
Out of focus, Partially blurred, Sharp
During
WSI
digitization
Applications :
Saving time, increasing the quality
Identification and reacquisition of blurred tiles during the
scan
Certification of the WSIs general image quality
Just after
WSI
digitization
Reacquisition of the WSI with more suitable profiles
Notification sent to reacquire the WSI
Continuous
Quality
Assusrance
Notification sent to recalibrate the WSI acquisition system
WSI quality scoring integrated in the files metadata
C++
Library
Implementations
Scaling
Optimized, multi-core, multi-node
Highly scalable to match any throughput
APIs
C++
Java
Python
Embeddable in Whole Slide Image acquisition systems
Embeddable in Whole Slide Image management platforms
Embeddable in Whole Slide Image viewers
Our references
Talk, 11th European Congress on Telepathology
5th International Congress on Virtual Microscopy
6-9 June 2012, Venice, Italy
Poster, Pathology Visions Conference,
October, 28-31, 2012, Baltimore, MA, USA.
Talk, 12th European Congress on Digital Pathology
18-21 June 2014, Paris, France
FlexMIm - Projet R&D - 4 989 K
Fonds Unique Interministriel n 14
2013-2015, Paris, France.
Talk, Pathology Visions Conference,
October, 20-21, 2014, San Francisco, CA, USA.
pre-seed funding
Contact :

Laboratory : David Ameisen - david.ameisen@gmail.com
Idfinnov : Robert Marino rmo@idfinnov.com