Re: 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-tp5008670p5008713.html

Hi Jan, 

Thank you for getting back to me so quickly! I am working on implementing the plugin and am currently trying to figure out how to use the plugin while running the macro in batch mode (the plugin requires selecting two separate files, both of which must be slightly different variations of one another). Do you have any ideas? 

Thank you again!!

- Danny Rosenberg -

On Fri, Jul 11, 2014 at 6:46 AM, gankaku [via ImageJ] <[hidden email]> wrote:

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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