http://imagej.273.s1.nabble.com/Linking-ROI-within-ROI-to-one-another-and-getting-an-output-tp5008670p5008735.html
> Jan,
>
> The plugin seems to be working really well, and looks like a much better
> solution to what I am working on than what I have been currently doing. I
> think I can figure out how to build a macro that properly creates two
> binary images the way I need them, and then runs the plugin, but I am not
> sure how to implement the macro on a wider scale when using batch mode (in
> other words, each image will have to be duplicated and processed slightly
> differently before being analyzed via Speckle Inspector), which means the
> macro will need to know each new file's unique name.
>
> - Danny
>
>
>
> On Mon, Jul 14, 2014 at 3:25 PM, gankaku [via ImageJ] <
>
[hidden email]> wrote:
>
> > Hi Danny
> >
> > You need the image with your small features you want to analyze per ROI
> as
> > binary image and another binary image which corresponds to your ROIs. You
> > can get this by either processing your image in a way which (after
> > applying
> > an Autothreshold) will give you the desired binary output or (if this is
> > not possible) you can create your ROIs manually, transfer them to a black
> > image of the same size as the first one and simply fill your ROIs with
> the
> > white foreground color.
> >
> > Those two images you can then use as input for the Speckle Inspector.
> >
> > Please check out the explanation for it, there you will see, how those
> two
> > images have to look like (
> >
http://fiji.sc/BioVoxxel_Toolbox#Speckle_Inspector).
> > Alternatively, post an example image and we might be able to help you
> with
> > further concrete suggestions. This will be way more helpful for you since
> > it deals with your data and the related difficulties.
> >
> > regards,
> >
> > Jan
> >
> >
> >
> >
> > Am 14.07.201417:23 schrieb "dprosenberg" <[hidden email]
> > <
http://user/SendEmail.jtp?type=node&node=5008724&i=0>>:
> >
> > > 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] <
http://user/SendEmail.jtp?type=node&node=5008724&i=1>>
> > 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]
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> > > > > 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]
> > > > <
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> > > > inquiries: [hidden email]
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> > > > web: www.biovoxxel.de
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