MASSACHUSETTS
GENERAL HOSPITAL
HARVARD
MEDICAL SCHOOL
PATHOLOGY
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
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
How to improve the color
accuracy of digital images?
By Color calibration???
MASSACHUSETTS
GENERAL HOSPITAL
PATHOLOGY
HARVARD
MEDICAL SCHOOL
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.
Objective
To perform an initial
investigation o
color standardization in whole
slide imaging using a
color chart..
MASSACHUSETTS
GENERAL HOSPITAL
PATHOLOGY
HARVARD
MEDICAL SCHOOL
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
Set of Color
filters
 The filters works well with H&E stained
slides
The color calibration slide for whole slide scanner
Calibration
slide for
use in
microscope
This is
Manually
made
HARVARD
MEDICAL SCHOOL
Method
Uncorrected
Image
Polynomial
transformation
Polynomial function:
Gamma
correction
Corrected
Image
Polynomial transformation
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
HARVAR
D
MEDICAL
SCHOOL
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
Results on H&E stained
images…
MASSACHUSETTS
GENERAL HOSPITAL
PATHOLOGY
HARVARD
MEDICAL SCHOOL
Original Image
The color improves…
Gamma =1
Result of the color
standardization
Red blood
cells
Red blood
cells
Nucleus
Nucleus
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.
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.
Calibration slides…
 Color calibration slides – color chart
This is
Manually
made
HARVARD
MEDICAL SCHOOL
 H&E stained slide ( mouse embryo)
H&E stained slide of a mouse embryo
Optimally stained
MASSACHUSETTS
GENERAL HOSPITAL
PATHOLOGY
Using these two
slides would further
improve the current
results…
HARVARD
MEDICAL SCHOOL
Conclusions
 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
HARVARD
MEDICAL SCHOOL
Thank you……
MASSACHUSETTS
GENERAL HOSPITAL
PATHOLOGY
HARVARD
MEDICAL SCHOOL