Point tool add overlay to all slices in stack

imagej

#1

I am using imageJ to count specific stained cells in an image. I have different pictures, at different wavelengths to be certain that I am counting the right type of cells.

For this I want stack the images so I can scroll through them while counting. I am using the point tool with “auto-measure” and “add to overlay” to count and to see which cells are already counted.

However, when I do this, it adds the overlay to one slice. I would like to add the overlay to all slices in my stack. I know that this is possible with for examples the pencil tool, by enabling “paint on overlay” but I can not use this to count my cells.

Does anyone have any suggestions how I can count, and see the overlay in all slices?

Many thanks!


#2

@Joren90

This is an old thread here on the Forum you can check out:

Perhaps the answer to your question is there regarding the overlay issue… it will most likely involve writing a small script.

eta


#3

It’s been a while, and I stopped working on this for some time, but I’ve resolved my issue.

For anyone who ever needs something like this, this is the macro code I use:

 macro "measure through stack" {
       saveSettings;
       setOption("Stack position", true);
       for (n=1; n<=nSlices; n++) {
          setSlice(n);
          run("Measure");
      }

It’s very simple. It just executes the measure command on every slice in the stack.
I installed it in my imageJ, and gave it a short key for easy use.