When i read your question it came to my mind that carbon nanoparticles are photoluminescent. Perhaps you can track them using their fluorescence . This way you may not need to label them wit a chromophore. Have you considered this option?
Thanks Jose for the answer. Do you have any links i can read more about it? never tried it but i need the label because some of the cells i am using with have their own autofloresence as well. So if you have anything about their own autoflorecense it would be great.