The ideal way of improving intonation is unison playing with an experienced musician who has great intonation. Finding experienced musicians with ample time for unison playing is tricky though!
Intonation Doctor is a clever new piece of software that plays along with you — but in tune. This gives you instant aural feedback and helps your intonation to correct itself in a natural way. Your corrections will be instinctive, rather than the intellectual corrections that you make when you're watching a tuner.
More importantly, because you can leave Intonation Doctor running the whole time you are practicing, you are receiving constant feedback with everything you are working on. Intonation practice is no longer an isolated exercise but an integrated, organic part of your playing time.