Hello,
Using the IMAQ WindROIColor function, you can select the color to use to depict ROI contours in the image window. This will change the color used for that particular window and will be the same for all the ROIs drawn. Currently there's no easy way of displaying each ROI with a different color but you could write your application so that as soon as it detects a region selection, it'll change the ROI display color and bring up the ROI select window with the previous ROIs displayed while prompting for the next ROI.
I hope this helps. Let me know if you have further questions on this.
Regards,
Yusuf C.
Applications Engineering
National Instruments