Could you provide more details, please ? The 12 bit resolution for each of 3 RGB color component is not enough ? How fast do you change the detectable object ? How is the light source ? What is the color range needed to detect ? Sorry for so much questions, but in last years I done a lot of test devices for Sony Bravia TV boards, where I detected the LEDs color, and I had to solve a lot of torubble around ambient light, etc., and I thing that these information are necessary to start similar project.
Regards
Zoltan
P.S.
Today I have got again a 6 LED/board color detection. I have designed an aprox. 5*8cm board with detectors and microcontroller which are pressed manually (pins contacts) to the tested pcb and switching on the LEDs and measuring the color of each one and make a decision PASS/FAIL indicating with a Green LED. If you want I can send you pictures about the proto and 2 weeks later about the final version.