Determining the position of the calcium ion in the three dimensional space Is it possible to determine the position of a single calcium ion or its population in the context of a three dimensional space with relatively good time frequency, say 1 Hz, taking into account possible dense presence of the other types of ions in the neighborhood?

The qeustion is asked in the strong relation to the nervous system, but any pure-theory or computer-simulation driven concepts are also welcome.
It is generally not possible to measure where a single calcium ion is in three dimensional space. However, it is possible to measure relative calcium ion concentration across a population of neurons using Two-Photon-Microscopy.

I stress relative because it does not give you an exact concentration of Calcium in terms of micro-molar concentration. However it is good enough to extract relative spike times of a individual neurons within the population. 

The way "Calcium Imaging" works is the experimenter loads a neuron or population of neurons with a fluorescing dye that "lights up"  in the presence of calcium. There are many such chemicals which are listed in this article here. The one I personally see being used in articles a lot is FURA-2. 

As for frequency it depends on the experiment typically range from 60Hz to 490 Hz.Be aware however the faster the sample rate is the more noise in the measurements. 

Do note that these methods are highly invasive, and require brain slices in vitro or opening the skull in vivo. As far as I am aware no study has been done on live humans. Typically rats are used.