How to measure nearest neighbor distances

Is there a way to measure nearest neighbor distances using ImageJ? The attached image is processed from a TEM image is shows nanoparticle clusters in black. I would like to measure the size and nearest neighbor distance for each particle. For size I used ferret length but cannot figure out how to measure the distance from nearest neighbor which should be a representation of particle density in a given area.


you can have a look at 3D Interactions from the 3D Suite, or there should also be something in the 3D manager. Have a look here for a similar question: FIJI ImageJ - Calculate neighbours for every connected object in an image - #3 by gabriel .

For that type of analysis you will need a label image - use Analyze Particles or another Connected Component labeling plugin to get it.

Possibly this thread could be worth to check out: