http://imagej.273.s1.nabble.com/Linking-ROI-within-ROI-to-one-another-and-getting-an-output-tp5008670p5008724.html
binary image and another binary image which corresponds to your ROIs. You
further concrete suggestions. This will be way more helpful for you since
> 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]
> > <
http://user/SendEmail.jtp?type=node&node=5008684&i=0>>:
> >
> > > 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]
> > <
http://user/SendEmail.jtp?type=node&node=5008684&i=1>>:
> > >
> > >> 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> > >>
> > >
> > >
> > >
> > > --
> > >
> > > CEO: Dr. rer. nat. Jan Brocher
> > > phone: +49 (0)6234 917 03 39
> > > mobile: +49 (0)176 705 746 81
> > > e-mail: [hidden email]
> > <
http://user/SendEmail.jtp?type=node&node=5008684&i=2>
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> > > inquiries: [hidden email]
> > <
http://user/SendEmail.jtp?type=node&node=5008684&i=4>
> > > web: www.biovoxxel.de
> > >
> >
> >
> >
> > --
> >
> > CEO: Dr. rer. nat. Jan Brocher
> > phone: +49 (0)6234 917 03 39
> > mobile: +49 (0)176 705 746 81
> > e-mail: [hidden email]
> > <
http://user/SendEmail.jtp?type=node&node=5008684&i=5>
> > info: [hidden email]
> > <
http://user/SendEmail.jtp?type=node&node=5008684&i=6>
> > inquiries: [hidden email]
> > <
http://user/SendEmail.jtp?type=node&node=5008684&i=7>
> > web: www.biovoxxel.de
> >
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> >
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