harvard medical school anurag sharma 1, mark merren 2, pinky bautista 2, roy lee 2 and yukako yagi 2...
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HARVARDMEDICAL SCHOOL
Anurag Sharma1, Mark Merren2, Pinky Bautista2, Roy Lee2 and Yukako Yagi2
The Effects of Compression Factor on The Effects of Compression Factor on Special Stains Whole Slide ImagingSpecial Stains Whole Slide Imaging
1 NEC Laboratories America, Inc.
2 Massachusetts General Hospital.
(Pathology Imaging & Comm. Tech. Center)
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HARVARDMEDICAL SCHOOL
Objective
To investigate the balance between quality and compression
To find appropriate compression for special stains in high volume Whole Slide Imaging (WSI)
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Background – WSI
WSI – Tasks and Expectations
Scan
Capture
Storage
Access
Quality
Reliability
Fast Scan Time
Less Storage Space
Quick Retrieval
Network/Internet
One factor that affects efficiency of a WSI system in many ways is
Image Compression
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Compression: Quality Factor (QF)
Background – Image Compression
No universal definition
Indicator of the image quality
Inversely proportional to the compression
Most scanners can be configured to change QF
QF 100 being the best quality image
Higher QF has higher infrastructure requirements
QF varies from manufacturer to manufacturer
Only factor user can control
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Effect of QF on Image Size
Quality versus size
QF 90 80 50 30 Screen shots
MB 692 391 220 189
MB 656 361 219 154
Image size and quality both get reduced with lower QF
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Why Special Stains
Earlier, we conducted a similar study with H&E where QF80 was found acceptable
Color distribution is more important than morphology
Special stains may work with higher compression
10-15% of slides/day is Special stain
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Material
Eight slides from Set I Trichrome
GMS
PAS-D
Reticulin
Mucicarmine
PAS
Elastic
Congo Red
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Material
Eight slides from Set 2
TrichromeGMSSteiner
BrownHopps-GramPAS Warthin-Starry
Reticulin
Giemsa
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Method Eight slides of mouse embryo
Eight slides of human tissue
Twelve stains
Three scanners
Total Images – 208
Resolution 0.33-0.50 µm/pixel
Reviewed by a pathologist and 4 non-pathologists including an imaging specialist
reviewed a calibrated monitor
Uncompressed (TIFF)
QF 90, 80, 70, 50, 30 (JPEG)
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Results:
Image quality was clearly affected by compression lower than QF 50
However this did not influence the evaluation with special stain
Most stains were acceptable with QF 30 except Reticulin
All stains showed lighter contrast with compression. (higher compression -> lower contrast)
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QF 90
Results - Mouse Embryo
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Results - Mouse Embryo
QF 30
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Results - Reticulin
Bone Marrow – Hypocellular marrow with triline age hematopoiesis
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Results - Reticulin
Liver Core Biopsy
QF 30
QF 90 QF 70
QF 50
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Results - Trichrome
Endocardium Biopsy (right ventricle)
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Results - PAS/D
Renal Cell Carcinoma
QF 30
QF 90
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HARVARDMEDICAL SCHOOL
Results - PAS/D
Quality degradation from QF 90 to QF 30
QF 90
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Results - Mouse Embryo – Trichrome
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HARVARDMEDICAL SCHOOL
Results:
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Results:
Special stain images of acceptable quality at QF 30
QF 50 for Reticulin
Artifacts visibility is high at lower QFs
Significant reduction in resources
scan time
storage space
image viewing
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Conclusion and discussion
Though the QF 30 provided acceptable image quality for most special stains, some stains worked at QF 50. Hence, a setting of QF 50 is found suitable for volume WSI scans.
Future works:
Quantitative analysis of the image quality
Similar study in Immuno-stains
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Thanks!