An Ex-vivo Confocal Microscopy imaging examination may be acquired in both reflectance and fluorescence mode. The reflectance and fluorescent images are acquired simultaneously and are exactly spatially correlated. Both the reflectance and fluorescent images are encoded and stored as grey scale images. Speciality Confocal Microscopy image viewers display reflectance and fluorescent images using different color overlays and allow the user to toggle between reflectance and fluorescence images. A vendor may choose to also encode a duplicate of the reflectance and fluorescence images as RGB images to allow for non-specialty viewers to display the reflectance and fluorescent confocal microscopy images in a similar way to speciality viewers. The color images would be encoded as a Visible Light Image IOD or a Secondary Capture Image IOD, as they are designed only for non-specialty viewers (e.g., EMR Universal Viewers).