A more robust plugin that can optionally compute separation distances between edges, centroids and centers of mass can be found at http://imagej.nih.gov/ij/plugins/graph/index.html

This plugin computes the minimum distance between objects. The Results Table must be populated with XStart and YStart and the current image must be the mask used to create the Results Table.

Ben Tupper

The objects are defined using ImageJ's eight-connected boundaries computed by the Wand class. Specifying a Nearest Neighbor Distance will trigger the output of an additional table in the log window the identifies objects that are 'connected' by virtue of being within the neighborhood distance. Note that groups maybe chain-like such that two objects at opposite ends of the chain maybe much further apart from each other than the minimum distance specified. Even so, via connectivity, they are consider part of the same group.

Download Boundary_Separation.java to the plugins directory. Create a binary mask and analyze it (Analyze > Analyze particles…). Be sure to select the “Record starts” option of the Analyzer dialog so that the Results Table will be populated with XStart and YStart.