The pitches in the chords come from the 11-limit tonality diamond. The tonality diamond is a way of extending the just intonation tuning system. Just intonation derives pitches via (relatively) simple frequency ratios. For example, an octave is twice the frequency of the root pitch (as it is in most tuning systems), the fifth is 3/2 the frequency of the root, and the fourth is 4/3.
The tonality diamond can produce more and finer divisions of pitch than just intonation does while maintaining simple ratios. The 11-limit tonality diamond used here has thirty pitches between the root and the octave (inclusive), as opposed to a conventional tuning system's twelve.