Hello,
i would recommend you to use "R" (after your ImageJ measurements)
http://www.r-project.org/with the "spatstat" package
http://www.spatstat.org/spatstat/which can calculate nearest neighbour distances in 3d, Ripley`s K function in 3d etc.
You can calculate it in Java (by yourself) but i think the spatstat package has many useful methods
already available for your analysis.