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A Study on Color Standardization in Whole Slide Imaging

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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  1. MASSACHUSETTS GENERAL HOSPITAL PATHOLOGY HARVARDMEDICAL SCHOOL A Study on Color Standardization in Whole Slide Imaging Pinky A. Bautista and YukakoYagi

  2. Color standardization -- Important aspect in the implementation of digital pathology Variations in digital slide colors

  3. 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

  4. MASSACHUSETTS GENERAL HOSPITAL PATHOLOGY HARVARDMEDICAL SCHOOL How to improve the color accuracy of digital images? By Color calibration???

  5. 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

  6. 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.

  7. MASSACHUSETTS GENERAL HOSPITAL PATHOLOGY HARVARDMEDICAL SCHOOL Objective To perform an initial investigation o color standardization in whole slide imaging using a color chart..

  8. 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

  9. Method Uncorrected Image Polynomial transformation Gamma correction Corrected Image Polynomial function:

  10. 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

  11. 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

  12. MASSACHUSETTS GENERAL HOSPITAL PATHOLOGY HARVARDMEDICAL SCHOOL Results on H&E stained images…

  13. Result of the color standardization Original Image The color improves… Gamma =1

  14. 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.

  15. Result of the color standardization Original Image Texture pattern is clearer…

  16. Result of the color standardization Original Image The color attributes of the tissue components improves

  17. Result of the color standardization Original Image The nuclei are clearly delineated…

  18. 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.

  19. 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

  20. 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.

  21. MASSACHUSETTS GENERAL HOSPITAL PATHOLOGY HARVARDMEDICAL SCHOOL Thank you……

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