The shadows are caused by the lamp being off to one side or the other of the scanner ( eye/Pickup ) and it is seeing a 3 dimentional image. The eye will be under thechip but the light is coming from the side slightly. You will notice the other side of the chip has no shadow.

Color;

You will have to play with the brightness/intensity/contrast to get the colors to come out accuratly. It does take some playing around to get accuracy.

Paul