Distance based colocalization of multi-point tool points in FIJI/ImageJ

Hi all,

I have a pretty basic question that I couldn’t find an answer to after a lot of googling.

I have multi-channel single slice images, and points made with the multi-point tool with a separate counter for each channel.

E.g., points counting cells which have fluorescently labelled puncta ‘A’ in channel 0 are represented by points in Counter 0 in the points tool, and counts representing cells with puncta ‘B’ in channel 1 are represented by points in Counter 1 in the points tool.

I would like to set a short distance, e.g. 20 nm (or pixel equivalent), and know how many points from Counter 0 are within that distance to points from Counter 1.

TL;DR edition:

The multi-points tool has multiple counters.

How can you count how many points in Counter 0 are within distance x from points in Counter 1?


Could you share a file with your point counts? Perhaps this will help setup a protocol



OK so it is a pain to play with multi-label points in macro language.

Basically, you have to run ‘Measure’, then re-import everything from the Results Table in a macro and do the analysis.

Thought it would be easier in Groovy, but the API for spots is a bit messy but we have something :slight_smile: :

Provided this example dataset
blobs_with_2_counters.tif (66.1 KB)

This code:

Will output something like this, depending on the value of Distance.

Code is not super obvious but hopefully it helps to get started.



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@oburri awesome thank you so much!

I will play around with this code when I have time and let you know how I fare.

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Hi, just letting you know that for my purposes it was quicker to just show all sets of points and add an extra set of points manually to count the existing points that are close together. I don’t have that many images to process so this’ll be faster for me.

If I have to do more in future I’ll try this code, thanks.

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