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

Posted by gankaku on
URL: http://imagej.273.s1.nabble.com/Linking-ROI-within-ROI-to-one-another-and-getting-an-output-tp5008670p5008675.html

Hi Danny,

actually I forgot in my last reply to the mailing list, that you can use
the RoiManager output after the Speckle Inspector to run the Analyze
Particles on each individual Roi. You might be able to do this with a macro
like this:

run("Set Measurements...", "area mean standard modal min centroid center
perimeter bounding fit shape feret's integrated median skewness kurtosis
area_fraction stack display redirect=None decimal=3");
counter = roiManager("count");
for(n=0; n<counter;n++) {
roiManager("select", n);
run("Analyze Particles...", "display");
}


regards,
Jan





2014-07-10 18:28 GMT+02:00 dprosenberg <[hidden email]>:

> 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?
>
> <http://imagej.1557.x6.nabble.com/file/n5008670/Untitled_1.jpg>
>
> Thanks,
> - Danny
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Linking-ROI-within-ROI-to-one-another-and-getting-an-output-tp5008670.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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