Anurag Sharma1, Mark Merren2, Pinky Bautista2, Roy Lee2 and Yukako Yagi2

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The Effects of Compression Factor on Special
Stains Whole Slide Imaging
Anurag Sharma1, Mark Merren2, Pinky Bautista2,
Roy Lee2 and Yukako Yagi2
1 NEC Laboratories America, Inc. 2 Massachusetts
General Hospital. (Pathology Imaging Comm.
Tech. Center)
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Objective

• To find appropriate compression for special
  stains in high volume Whole Slide Imaging (WSI)

• To investigate the balance between quality and
  compression

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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 One factor that affects efficiency of a WSI system in many ways is Image Compression

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Background Image Compression
Compression Quality Factor (QF)

• 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 HE
  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
PAS-D
Elastic
GMS
Congo Red
Reticulin
PAS
Mucicarmine
Eight slides from Set I
Trichrome
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Material
BrownHopps-Gram
Giemsa
PAS
Warthin-Starry
Trichrome
GMS
Steiner
Reticulin
Eight slides from Set 2
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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 -gt lower
  contrast)

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QF 90
Results - Mouse Embryo
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QF 30
Results - Mouse Embryo
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Results - Reticulin
Bone Marrow Hypocellular marrow with triline
age hematopoiesis
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Results - Reticulin
QF 70
QF 90
QF 30
QF 50
Liver Core Biopsy
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Results - Trichrome
Endocardium Biopsy (right ventricle)
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Results - PAS/D
QF 30
QF 90
Renal Cell Carcinoma
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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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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!