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-tp5008670p5008684.html

Hi Danny, hi everyone,

I further updated the "Speckle Inspector
<http://fiji.sc/BioVoxxel_Toolbox#Speckle_Inspector>". Now you can also get
a detailed analysis of all small objects in each ROI (from a bigger object)
in a results table if desired.

I am happy about any feedback.

regards,
Jan


2014-07-10 21:56 GMT+02:00 BioVoxxel <[hidden email]>:

> 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.
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
>
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