Find maxima in 3D ROIs

Dear all,

I’m writing a macro for FIJI to count the number of maxima peaks in 3D stacks, within multiple individual ROIs (corresponding to multiple individual nuclei that are present in the images, segmented as 3D ROIs).

Does exist a way to redirect the “3D maxima finder” plugin (or similar) to 3D ROIs?

My final aim is to have “peaks per nucleus”, working with 3D images.

Your help will be really appreciated!!

Thanks in advance,


Dear @michiroc,

If you are referring to the 3DManager, there is an option for numbering. This option is available in options, how does it work :

  1. Open your labelled image with the nuclei
  2. Add it to the 3DManager
  3. Open your labelled image with peaks
  4. Be sure to select the image with peak and perform Quantif3D
  5. The number of peaks and the volume occupied by peaks will be computed for each nuclei

Hope this helps,



Hi Thomas,
thanks a lot for you kind reply and your help!

Can I ask for another questions?
If I want to analyze small particles size and/or their individual intensity and not just count them in the nuclei, do you know if there is a way to have these information per particle, per nucleus?
I mean to be able to know for example the size distribution of the particles in nucleus A, nucleus B, nucleus C and so on…

Thanks a lot!!

Hi @michiroc,

You are welcome. Actually we developed TANGO a few years ago to analyse nuclear organization, if you are comfortable installing MongoDB database you can try to install TANGO.

Alternatively, usually I also have another approach :

  1. Open labelled particles image
  2. Add to 3DManager
  3. Perform measurements (volume, shape, …)
  4. Open and select intensity image for particles
  5. Perform quantifications (intensity measurements)
  6. Open and select labelled nuclei image
  7. Perform quantification (this will give you the value of the nucleus the particles are within)

Hope this helps,