Method and system for whole slide imaging

A system for obtaining an adapted calibration transformation for whole slide imaging, wherein the adapted calibration transformation is for outputting the color of an empty area of the slide in a whole slide image WSI obtained by a scanner as a desired color in a device-independent color space, the system comprising:

• a scanner for obtaining a WSI in a device-dependent color space;
• a processor configured to:
• receive a color target WSI in a device-dependent color space, wherein the color target WSI is a WSI of a color target from the scanner represented in the device-dependent color space and wherein the color target contains at least a white patch and three color patches;
• obtain a calibration transformation for transforming the device-dependent color space to a device-independent color space based on calibrating the scanner by mapping a set of scanner acquired raw RGB values from the color target with a set of reference colorimetric values to obtaining the calibration transformation;
• determine a chromatic adaptation transformation based on the color of the white patch in the device-dependent color space, the color of the empty area in the device-dependent color space and the desired color in a target color space;
• and
• obtain an adapted calibration transformation based on applying the chromatic adaptation transformation to the calibration transformation.