Zzman,
I am sorry you got such a rude answer from nbucska. I think he may have misunderstood your problem. Reading between the lines it seem that since you are a bioengineer the experiment has all sorts of wet and gooey stuff in it, moving around "under its own steam", possibly with fixed organic material as well. This precludes any (visible) optical sensing.
I think the problem is this, as you decrease the frequency of the electromagnetic wave you increase the wavelength. Trying to measure positions using "low frequency" electromagnetic fields is like trying to do watch repairs whilst wearing boxing gloves.
Light is a nice high frequency electromagnetic wave, giving plenty of resolution. Radio waves at say 300MHz have a wavelength of 1m and are therefore somewhat coarse for your experiment. The trouble with higher frequency waves, which have a higher photon energy, is that they may just pass right through your target objects. Xrays for example would go through organic material to a greater or lesser degree. Thus the first thing you would want to do would be to "tag" the items in question with a piece of metal or a miniature transponder of some sort. If the movement required is only 2mm I have to guess that the object is small as well.
If you can fill in some blanks and let us know what you are trying to do more explicitly we may be able to help, or at least advise definitely that the idea is not going to be very workable. Mostly it is a question of cost. It might mean you need a Terawave imaging system for example, and this would be beyond the financial reach of most users. Maybe you need a small radio-isotope system, but this might be beyond the safety limitations inside cities. There are often solutions, they just may be prohibitively expensive.