Problem with NND plugin in Fiji

Hello all. I hope there is a simple fix for this.

I have been using the NND plugin for Fiji successfully for a few years but this week it has stopped working for me and I get a pop-up message window that says ‘results table appears to be empty’.

I really don’t know how to fix this and was hoping that someone might have a simple solution.

I have attached an image of the message I get when running the plugin and also a link to the plugin itself and the webpage associated with it.

Many thanks,


NND Plugin Page

Link to download plugin:


I have invited the author of the plugin to this thread… hopefully, he responds here. But in the meantime - you can:

  1. send him an email directly … but in this case, please report back the solution/answer here on the forum so the whole community can benefit.

  2. try another tool … The BioVoxxel Toolbox has a feature for calculating nearest neighbors: Nearest Neighbor Indicator This of course depends on the analysis you are doing and what you need as output…

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I am still having this problem with the NND plugin and the author has not responded to either my direct email or this thread. So I was wondering if anyone has any suggestions? Thanks.

The nearest neighbor indicator unfortunatly does not allow to calculate or read out the nnd distance. :frowning:

You can also have a look at the 3D ROI Manager which also works for 2D images. It can read out distances between all objects as well.

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I’ve actually found a solution to my problem by inverting the binarised image prior to running the NND plugin. I have no idea why this is needed or how it fixes the problem but I thought I would let any other users know my work-around.

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