Microscopes typically use a single color illumination source and the intensity of it can be varied depending on the application. They are used to observe various specimens which are usually stained to highlight the objects of interest. Automatic methods for identification of diseases from these specimens have been developed recently. The stains result in different colors and white illumination source may not offer the best contrast in all cases. Further, the staining process does not always result in the same color owing to the changes in the pH of the buffer used. This paper overcomes these problems by using a varying color illumination source for microscopes to offset the variations in the stain and ensures that the best contrast is achieved under all conditions. The results of segmentation of nucleus of White Blood Cells under varying color illuminations are shown as an example.