I am trying to use the 3D object counter plugin from ImageJ to count and determine the volume of aggregate structures inside cells imaged with LSM with Z stacks taken. Once I set all my parameters and threshold and prompt the program to do its calculations a summary table is generated as well as an image that allows me to scroll through all of the Z stacks and see which structures have been counted. The problem is that as I go along the Z stacks I see that dots that are obviously parts of the same aggregate have been counted as separate entities. What is a way to resolve this problem? Is it possible that our Z stacks are too far apart? If so, how should we take our Z stacks in order for the counter to interpret dots with the same XY coordinates but different Z coordinate as part of the same aggregated structure?