Following protein puncta across time points


I am Sahana from India. I have images of neurons labelled with GFP and a protein which is expressed in these neurons labelled with mCherry(Cx35-mCherry). My experiment involves following the movement of Cx35 puncta across time points w.r.t. the growth of the neuronal processes (dendrites).
I am quite comfortable with tracing out the neuron using SNT and giving each branch an identity using their x,y,z coordinates. I would like to do the same for the puncta. I have been using cell profiler to get the x,y coordinates of these punctae, but I also want their z-coordinates. Could anyone please let me know which is the best plugin for that? Any help would be really appreciated.