How to utilize ImageJ to count foci per nucleus



Original tif image: download

Hello all! I have been utilizing ImageJ to count foci per nucleus manually. However, as you all know that manually counting foci is extremely consuming. I do utilize find maxima however, it doesn’t count everything. I was hoping to find a more automated process to count foci per nucleus utilizing ImageJ. I am relatively new to utilizing ImageJ. Every suggestion would be greatful!



Do you have another nuclei-specific marker (DAPI or such?) for these images? That would be ideal… to first delineate (ie - segment) your nuclei with a more consistent (across all cells) marker such as DAPI and then use those ROIs to search for punctate/foci staining within.

Too - which are the ‘foci’ that you wish to count? The single bright spots? Or more?

And being new to ImageJ - no worries there! Here are some really helpful links to get you started:

For Scripting - ie. writing macro code - here are some other helpful links:

I hope this helps a bit! Just let us know… we are here to help.


Fibrosis analysis: masson trichrome. Macro not running

Yes I do have DAPI and yes I would like to count the bright spots. What I have been doing is adjusting the image brightness/ contrast then utilize find maxima then manually count the rest. Thank you for the links


Please post a typical image. Imprecise request lead to imprecise suggestions.


Merged (DAPI, Red and Green)


In the bottom cell, how many are red and how many are green dots? I can see 1 of each large ones, but many small ones.


Hi Gabriel,
For the entire picture, I counted 15 nucleus with 290 foci for green. I have not gotten a chance to count the red yet.


Thank you for the links. I will take a look at them and go through them.



If you have more questions - once you come up with an analysis workflow - just ask again! We are here to help!

eta :slight_smile:


Have a look at the speckle inspector from the BioVoxxel Toolbox: