HARVARD MEDICAL SCHOOL Anurag Sharma 1, Mark Merren 2, Pinky Bautista 2, Roy Lee 2 and Yukako Yagi 2...

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)


Objective

To investigate the balance between quality and compression

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


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


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


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


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


Material

Eight slides from Set I Trichrome

GMS

PAS-D

Reticulin

Mucicarmine

PAS

Elastic

Congo Red


Material

Eight slides from Set 2

TrichromeGMSSteiner

BrownHopps-GramPAS Warthin-Starry

Reticulin

Giemsa


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)


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)


QF 90

Results - Mouse Embryo


Results - Mouse Embryo

QF 30


Results - Reticulin

Bone Marrow – Hypocellular marrow with triline age hematopoiesis


Results - Reticulin

Liver Core Biopsy

QF 30

QF 90 QF 70

QF 50


Results - Trichrome

Endocardium Biopsy (right ventricle)


Results - PAS/D

Renal Cell Carcinoma

QF 30

QF 90


Results - PAS/D

Quality degradation from QF 90 to QF 30

QF 90


Results - Mouse Embryo – Trichrome


Results:


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


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


Thanks!

HARVARD MEDICAL SCHOOL Anurag Sharma 1, Mark Merren 2, Pinky Bautista 2, Roy Lee 2 and Yukako Yagi 2...

Documents

Transcript of HARVARD MEDICAL SCHOOL Anurag Sharma 1, Mark Merren 2, Pinky Bautista 2, Roy Lee 2 and Yukako Yagi 2...