a study on color standardization in whole slide imaging
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A Study on Color Standardization in Whole
Slide Imaging
Pinky A. Bautista and Yukako Yagi
MASSACHUSETTSGENERAL HOSPITAL
PATHOLOGY
HARVARDMEDICAL SCHOOL
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)
Whole slide
scanner 2 (WSI 2)
What is the cause of the
color variations??
H&E stained images
The same tissue slide scanned by different scanners .
How to improve the color accuracy of digital images?
MASSACHUSETTSGENERAL HOSPITAL
PATHOLOGY
HARVARDMEDICAL SCHOOL
By Color calibration???
Color chart-- Physical arrangement of standardized color samples
Used for color comparison measurements
Used for Checking color reproduction of an imaging system.
Used to calibrate and to profile graphic devices
The theoretical RGB values are stored and compared to measured values….
Color chart in medical applications
1. Sven Van Poucke et al,” Automatic colorimetric calibration of human wounds”, BMC Medical imaging, 2010,10:7
The color chart is utilized to calibrate images of wound
captured at different lighting condition
1
2. C. Grana et al , “ Color calibration for a Dermatological Video Camera System”, proc. Intl. Conference on Pattern Recognition (ICPR) 2004.
2
lesion Images captured with two different imaging system Corrected
color
Objective
MASSACHUSETTSGENERAL HOSPITAL
PATHOLOGY
HARVARDMEDICAL SCHOOL
To perform an initial investigation o
color standardization in whole slide imaging using a
color chart..
Calibration slide for use in microscope
Set of Color filters
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)
9 color filters were selected for Histology Stained Slides The filters were identified in previous study The filters works well with H&E stained slides
HARVARDMEDICAL SCHOOL
The color calibration slide for whole slide scanner
This is Manually made
MethodUncorrected
ImagePolynomial transformation
Gamma correction
Corrected Image
Polynomial function:
Polynomial transformation
HARVARD
MEDICAL
SCHOOLReference color of the color patches
Color of the patches as produced by a particular scanner
Each scanner will have its own Color transformation matrix
Color transformation matrix will be stored for used in color standardization
Color patches
Original Reference
Standardize using the original and reference color patches
Original Reference
Original - Produced by a whole slide scanner
Colors are not accurate enough
Reference - Produced by using spectral information of the patches
MASSACHUSETTSGENERAL HOSPITAL
PATHOLOGY
HARVARDMEDICAL SCHOOL
Results on H&E stained images…
Original Image Result of the color standardization
The color improves…Gamma =1
Original Image Result of the color standardization
Contrast between nuclei and other eosin stained tissue structures becomes better; color of red blood cells has been enhanced.
Red blood cells
Red blood cells
Nucleus Nucleus
Original Image Result of the color standardization
Texture pattern is clearer…
Original Image Result of the color standardization
The color attributes of the tissue components improves
Original Image Result of the color standardization
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.
MASSACHUSETTSGENERAL HOSPITAL
PATHOLOGY
HARVARDMEDICAL SCHOOL
HARVARDMEDICAL SCHOOL
This is Manually made
Using these two slides would further improve the current results…
Calibration slides… Color calibration slides – color chart
H&E stained slide ( mouse embryo)
H&E stained slide of a mouse embryoOptimally stained
Conclusions
MASSACHUSETTSGENERAL HOSPITAL
PATHOLOGY
HARVARDMEDICAL SCHOOL
Utilization of a calibration slide is practical and easy to implement to standardized the color of digital slides
Color standardization of digital slides is possible using the color calibration slide
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.
MASSACHUSETTSGENERAL HOSPITAL
PATHOLOGY
HARVARDMEDICAL SCHOOL
Thank you……
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