Linking ROI within ROI to one another (and getting an output)

Posted by dprosenberg on
URL: http://imagej.273.s1.nabble.com/Linking-ROI-within-ROI-to-one-another-and-getting-an-output-tp5008670.html

This is a repost (I originally posted a few weeks ago but I don't think the message was ever sent to the mailing list).

I am working on a macro using my limited knowledge of ImageJ in order to analyze cell nuclei and specific features within the nuclei.

I am thresholding images twice, the first time to get a general ROI that surrounds a cell's nucleus, and then I am reverting the image and rethresholding within the bounds of the original ROIs in order to get smaller ROIs that surround the nuclear holes (of which there can be multiple within each nucleus). The ultimate goal is to be able to get measurement data for both the nuclei and the holes, which I have had success doing, but I can't seem to figure out an easy way to link the nuclear holes to their "parent" nuclei.

Is there any way that FIJI/ImageJ can recognize an ROI within an ROI and provide some sort of output?



Thanks,
- Danny