A study on color standardization in whole slide imaging
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MASSACHUSETTS GENERAL HOSPITAL. PATHOLOGY. HARVARD MEDICAL SCHOOL. A Study on Color Standardization in Whole Slide Imaging. Pinky A. Bautista and Yukako Yagi. Color standardization . -- Important aspect in the implementation of digital pathology. Variations in digital slide colors.

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A Study on Color Standardization in Whole Slide Imaging

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MASSACHUSETTS

GENERAL HOSPITAL

PATHOLOGY

HARVARDMEDICAL SCHOOL

A Study on Color Standardization in Whole Slide Imaging

Pinky A. Bautista and YukakoYagi


Color standardization

-- Important aspect in the implementation of digital pathology

Variations in digital slide colors


Whole slide scanners and Color Imaging

Whole slide scanner 1 (WSI 1)

The same tissue slide scanned by different scanners .

What is the cause of the color variations??

Whole slide scanner 2 (WSI 2)

H&E stained images


MASSACHUSETTS

GENERAL HOSPITAL

PATHOLOGY

HARVARDMEDICAL SCHOOL

How to improve the color accuracy of digital images?

By Color calibration???


Color chart

-- Physical arrangement of standardized color samples

The theoretical RGB values are stored and compared to measured values….

  • Used for Checking color reproduction of an imaging system.

  • Used for color comparison measurements

  • Used to calibrate and to profile graphic devices


Color chart in medical applications

The color chart is utilized to calibrate images of wound captured at different lighting condition

1

lesion Images captured with two different imaging system

Corrected

color

2

1. Sven Van Poucke et al,” Automatic colorimetric calibration of human wounds”, BMC Medical imaging, 2010,10:7

2. C. Grana et al , “ Color calibration for a Dermatological Video Camera System”, proc. Intl. Conference on Pattern

Recognition (ICPR) 2004.


MASSACHUSETTS

GENERAL HOSPITAL

PATHOLOGY

HARVARDMEDICAL SCHOOL

Objective

To perform an initial investigation o

color standardization in whole slide imaging using a

color chart..


Yagi Adaptation Color Calibration Slide

(Overview of telepathology, virtual microscopy, and whole

slide imaging: prospects for the future, Ronald Weinstein et al. In Human Pathology, 2009)

HARVARDMEDICAL SCHOOL

The color calibration slide for whole slide scanner

  • 9 color filters were selected for Histology Stained Slides

Calibration slide for use in microscope

  • The filters were identified in previous study

  • The filters works well with H&E stained slides

Set of Color filters

This is Manually made


Method

Uncorrected Image

Polynomial transformation

Gamma correction

Corrected Image

Polynomial function:


Polynomial transformation

HARVARDMEDICAL SCHOOL

Color of the patches as produced by a particular scanner

Reference color of the color patches

Color transformation matrix will be stored for used in color standardization

Each scanner will have its own Color transformation matrix


Color patches

  • Colors are not accurate enough

  • Standardize using the original and reference color patches

Original- Produced by a whole slide scanner

Reference- Produced by using spectral information of the patches

Original

Reference

Original

Reference


MASSACHUSETTS

GENERAL HOSPITAL

PATHOLOGY

HARVARDMEDICAL SCHOOL

Results on H&E stained images…


Result of the color standardization

Original Image

The color improves…

Gamma =1


Red blood cells

Red blood cells

Nucleus

Nucleus

Result of the color standardization

Original Image

Contrast between nuclei and other eosin stained tissue structures becomes better; color of red blood cells has been enhanced.


Result of the color standardization

Original Image

Texture pattern is clearer…


Result of the color standardization

Original Image

The color attributes of the tissue components improves


Result of the color standardization

Original Image

The nuclei are clearly delineated…


  • Regardless of the image composition, i.e. what type of tissue structures are present, the current color standardization equally results to improved color attributes of the image.

  • We can observed more details in the standardized image.


MASSACHUSETTS

GENERAL HOSPITAL

PATHOLOGY

HARVARDMEDICAL SCHOOL

HARVARDMEDICAL SCHOOL

Calibration slides…

  • Color calibration slides – color chart

  • H&E stained slide ( mouse embryo)

Using these two slides would further improve the current results…

H&E stained slide of a mouse embryo

This is Manually made

Optimally stained


Conclusions

MASSACHUSETTS

GENERAL HOSPITAL

PATHOLOGY

HARVARDMEDICAL SCHOOL

  • Color standardization of digital slides is possible using the color calibration slide

  • Utilization of a calibration slide is practical and easy to implement to standardized the color of digital slides

Future works

  • Include a grey-level balancing in the method and add neutral colors to the color calibration slide to further improve the results

  • Use the optimally stained embryo slide together with the color calibration slide

  • Extend the method to special stains.


MASSACHUSETTS

GENERAL HOSPITAL

PATHOLOGY

HARVARDMEDICAL SCHOOL

Thank you……


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