Flattening Multiple Overlays

Posted by alexwatson on Aug 08, 2011; 9:07pm
URL: http://imagej.273.s1.nabble.com/IJ-setAutoThreshold-tp3683573p3683575.html

Hello All,

I have an image stack with Overlays that correspond to individual slices.  Each Overlay contains some text ROIs.  I would like for my plug-in to flatten each individual Overlay onto its corresponding slice ONLY (not the whole stack!) and then save the image stack.  I like the result of the Overlay -> Flatten command, however I don't think that outputting each individual flattened image and then merging them all into a stack is a clean solution.  So, I was wondering if someone could give me some code to draw an Overlay onto a single slice in a stack.

Thanks in Advance,

Alex