A low light intensity makes it difficult to separate different colors, due to the form of the HSI color space. When it is not possible to use strong illumination in your setup, try using fluorescent marker colors with UV lighting.
For optimal color separation, illuminate your setup with lamps that approximate to daylight in color temperature. Color temperature (unit Kelvin) is a term from theoretical physics that corresponds to the temperature of a tungsten lamp filament. The higher the color temperature the richer the light is in bluish and the poorer it is in reddish rays and vice versa. Daylight at noon is rated at about 5500 K. The color temperature of tungsten lamps ranges between 2600 and 3400 K. Special fluorescent tubes (for example, Philips TLD type) exist with color temperatures around 5500 K.