While searching the subject of magnetometer calibration, I came upon MagCal, a software tool developed by the Position, Location And Navigation Group (PLAN) at the University of Calgary. I got the idea of developing my own implementation of such a tool, as part of the development of a custom compass.
Magneto, like MagCal, looks for the ellipsoid that best fits the magnetometer raw measurements. Magneto uses a technique known as "Li's ellipsoid specific fitting algorithm", described in this paper, and for which a Matlab implementation is available.
After the characteristics of the ellipsoid are established, a correction matrix can be developed. This Application Note has been a useful reference for this step.