How do the colours help the pupil?

Staff notation is a very beautiful invention. Experienced players can take one look, and immediately see everything they need to know in order to play and understand a piece. But it is an abstract system, and it can take a long time for a beginner to learn to read it fluently. Sometimes the first steps can be very daunting if, at the same time, most of the pupil’s mind is taken up with the physical problems of playing the instrument. Using colour can guide the eye, and focus the mind, in a quick and unfussy way.

In the case of string instruments, one way to use colour is to have a colour for each string. This breaks the stave up into small, manageable zones. Once directed to the right string, the beginner pupil only needs to make simple 2- or 3-way choices. The mental load is lightened, the pupil will “get to the the tune” with less effort, and the logic of the stave lines and spaces can be learned at a gradual pace.
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What about the transition to reading without colours?

If you teach a pupil to read music with coloured notes, will that pupil then find it difficult to read ordinary black notes?

In my own experience, most pupils who have worked through the first book of Rainbow Guitar (or Rainbow Ukulele) will find that they can make the switch to playing tunes with the same notes, printed black in the normal way, within a very short space of time and with very few problems.  If you have had a lot of practice in playing tunes which look like this:

then it is not really such a great leap to playing a tune which looks like this:

The fact that pupils can make this transition fairly quickly, and with few problems, is the real proof that this system works. The colours have been helping in the early stages, but they have not been doing all the work! The pupil has still had to learn how the stave works, and to focus constantly on its shapes, lines and spaces.