ImageJ - Re: Linking ROI within ROI to one another (and getting an output)

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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-tp5008670p5008725.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]>:

> 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: <a href="tel:%2B49%20%280%296234%20917%2003%2039" value="+4962349170339" target="_blank">+49 (0)6234 917 03 39
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> > > e-mail: [hidden email]

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> >
> >
> >
> > --
> >
> > CEO: Dr. rer. nat. Jan Brocher
> > phone: <a href="tel:%2B49%20%280%296234%20917%2003%2039" value="+4962349170339" target="_blank">+49 (0)6234 917 03 39
> > mobile: <a href="tel:%2B49%20%280%29176%20705%20746%2081" value="+4917670574681" target="_blank">+49 (0)176 705 746 81
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> >
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