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-tp5008670p5008674.html

Hi Danny,

You could try if the Speckle Inspector from the BioVoxxel Toolbox might
help you (http://fiji.sc/BioVoxxel_Toolbox#Speckle_Inspector). This plugin
is specifically designed to count small features inside bigger ones. This
is first of all only for counting. I will think about including a more
detailed analysis for more measurements besides the simple count statistics.

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
>
>
>
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> Sent from the ImageJ mailing list archive at Nabble.com.
>
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