Re: ROI analysis of image stack

Posted by Wayne Rasband on Jan 13, 2006; 6:12pm
URL: http://imagej.273.s1.nabble.com/ROI-analysis-of-image-stack-tp3704073p3704075.html

> A question regarding ROI analysis of Image Stack:
>
> I would like to draw ROI's, slice-by-slice, on an image stack
> and then convert to mask (i.e. fill inside, clear outside).
> Is there a plugin, or batch mode way to do this?

You can do this by adding the ROIs to the ROI Manager and then running
this macro:

   n = roiManager("count");
   for (i=0; i<n; i++) {
      roiManager('select', i);
      run("Clear Outside", "slice");
      run("Fill", "slice");
   }

Install the ROI Manager macro set at

     http://rsb.info.nih.gov/ij/macros/RoiManagerMacros.txt

and you will be able to add an ROI to the ROI Manager and advance to
the next slice by pressing "5".

-wayne