I have a time-dependent system of varying number of particles (~100k particles). In fact, each particle represents an interaction in a 3D space with a particular strength. Thus, each particle has (X,Y,Z;w) which is the coordinate plus a weight factor between 0 and 1, showing the strength of interaction in that coordinate. 
Here <http://pho.to/9Ztti> I have uploaded 10 real-time snapshots of the system, with particles are represented as reddish small dots; the redder the dot, the stronger the interaction is. 

The question is: how one can produce a 3D (spatial) density map of these particles, preferably in Matlab or Origin Pro 9 or [ImageJ](http://imagej.nih.gov/ij/)? Is there a way to, say, take the average of these images based on the red-color intensity in [ImageJ](http://imagej.nih.gov/ij/)?

Since I have the numerical data for particles (X,Y,Z;w) I can analyze those data in other software as well. So, you are welcome to suggest any other analytical approach/software

Any ideas/comments are welcome!