Annular ROI and profile plot

[MartinG]

Hi there,
I would like to define annular ROIs with a circular shape. Afterwards I want to plot a profile of the intensity, wich should be the average over the thickness of the ROI (according to the center of the circle). Is there any way to achieve such a plot with ImageJ?

thanks!
Martin

[Herbie-3]

Martin,

as far as I understand your request, you may try

        Edit > Selections > Make Band

after having made a proper initial circular selection.

Enter the desired ring width in "Make Band" and measure, undo "Make
Band" and redo using another ring width etc.

You can automate the process with an IJ-macro. Use

        Plugins > Macros > Record

to obtain the necessary routines.

HTH

Herbie

:::::::::::::::::::::::::::::::::
On 28.01.14 12:06, MartinG wrote:

> Hi there,
> I would like to define annular ROIs with a circular shape. Afterwards I want
> to plot a profile of the intensity, wich should be the average over the
> thickness of the ROI (according to the center of the circle). Is there any
> way to achieve such a plot with ImageJ?
>
> thanks!
> Martin
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Annular-ROI-and-profile-plot-tp5006314.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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[MartinG]

Thanks for the answer.

Unfortunately I want to get a different kind of information (a intensity distribution).
A similar profile can achived by using "segemented line slection", setting the "line width" to a certain amount, draw a shape around the desired area and plot profile afterwards.
Now I want to get something like that, but with a annual ROI instead of a lot of lines.

Martin

[Jan Eglinger]

Hi Martin,

On 28.01.2014, 1:07 PM, MartinG wrote:
> Unfortunately I want to get a different kind of information (a intensity
> distribution).
> A similar profile can achived by using "segemented line slection", setting
> the "line width" to a certain amount, draw a shape around the desired area
> and plot profile afterwards.
> Now I want to get something like that, but with a annual ROI instead of a
> lot of lines.
>

Double-click the Line Tool to set the line width to the desired
thickness of the annular selection. Then convert your circle selection
to a line using 'Edit > Selection > Area to Line' and plot its profile.

In a macro:

makeOval(30, 30, 50, 50); // or draw a circle selection manually
setLineWidth(10);
run("Area to Line");
run("Plot Profile");

Hope that helps,
Jan

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[Frederic V. Hessman]

Martin,

Before asking the net or re-inventing the wheel, you should always look at the list of standard external plugins first:

        http://rsb.info.nih.gov/ij/plugins/index.html

There are various “radial profile plot” options.  We also have one in the astronomy plugins.

Rick

On 28 Jan 2014, at 13:07, MartinG <[hidden email]> wrote:

> Thanks for the answer.
>
> Unfortunately I want to get a different kind of information (a intensity
> distribution).
> A similar profile can achived by using "segemented line slection", setting
> the "line width" to a certain amount, draw a shape around the desired area
> and plot profile afterwards.
> Now I want to get something like that, but with a annual ROI instead of a
> lot of lines.
>
> Martin
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Annular-ROI-and-profile-plot-tp5006314p5006316.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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[CARL Philippe (LBP)]

Dear Rick,
In the case you are interested in the radial profile plugin, I would rather
recommend you to use my extension version of the plugin:
        http://rsbweb.nih.gov/ij/plugins/radial-profile-ext.html
which gives you much more features and flexibility (by using the mouse
and/or keyboard | thanks a lot to Michael Schmid) in order to set the
position and dimension of the circular ROI.
Nevertheless what Martin was asking isn't going in the applications of these
plugins and I think, unless I'm wrong, that his question has been correctly
answered by Jan...
My best regards,
Philippe

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de
Frederic V. Hessman
Envoyé : mardi 28 janvier 2014 14:11
À : [hidden email]
Objet : Re: Annular ROI and profile plot

Martin,

Before asking the net or re-inventing the wheel, you should always look at
the list of standard external plugins first:

        http://rsb.info.nih.gov/ij/plugins/index.html

There are various “radial profile plot” options.  We also have one in the
astronomy plugins.

Rick

On 28 Jan 2014, at 13:07, MartinG <[hidden email]>
wrote:

> Thanks for the answer.
>
> Unfortunately I want to get a different kind of information (a
> intensity distribution).
> A similar profile can achived by using "segemented line slection",
> setting the "line width" to a certain amount, draw a shape around the
> desired area and plot profile afterwards.
> Now I want to get something like that, but with a annual ROI instead
> of a lot of lines.
>
> Martin
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Annular-ROI-and-profile-plot-tp500631
> 4p5006316.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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[Cammer, Michael]

Is this what you need?  Does not go all the way to the center, however.  Also, thanks to many new commands added to ImageJ over the years, the macros could be greatly simplified.

http://cammer.net/aecom/annuli/index.htm
User:  aecom
Pwd:  newpassword

Selected Annulus Method Publications:
Bailly M, Macaluso F, Cammer M, Chan A, Segall JE, Condeelis JS.  Relationship between Arp2/3 complex and the barbed ends of actin filaments at the leading edge of carcinoma cells after epidermal growth factor stimulation. J Cell Biol. 1999 Apr 19;145(2):331-45.
DesMarais V, Ichetovkin I, Condeelis J, Hitchcock-DeGregori SE.  Spatial regulation of actin dynamics: a tropomyosin-free, actin-rich compartment at the leading edge.  J Cell Sci. 2002 Dec 1;115(Pt 23):4649-60.


===========================================================================
Michael Cammer, Microscopy Core & Dustin Lab , Skirball Institute, NYU Langone Medical Center
Cell:  914-309-3270   Lab: 212-263-3208
http://ocs.med.nyu.edu/microscopy & http://www.med.nyu.edu/skirball-lab/dustinlab/

===========================================================================
Michael Cammer, Microscopy Core & Dustin Lab , Skirball Institute, NYU Langone Medical Center
Cell:  914-309-3270   Lab: 212-263-3208
http://ocs.med.nyu.edu/microscopy & http://www.med.nyu.edu/skirball-lab/dustinlab/

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of MartinG
Sent: Tuesday, January 28, 2014 6:07 AM
To: [hidden email]
Subject: Annular ROI and profile plot

Hi there,
I would like to define annular ROIs with a circular shape. Afterwards I want to plot a profile of the intensity, wich should be the average over the thickness of the ROI (according to the center of the circle). Is there any way to achieve such a plot with ImageJ?

thanks!
Martin



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View this message in context: http://imagej.1557.x6.nabble.com/Annular-ROI-and-profile-plot-tp5006314.html
Sent from the ImageJ mailing list archive at Nabble.com.

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[Jan Eglinger]

Dear all,

if understood Martin correctly, he is asking for a plot of

   Intensity vs. Angle  (can you call it circumferential profile?)

as opposed to a plot of

   Intensity vs. Distance from center (radial profile).


The plugin "Oval Profile Plot"[1] seems to provide this functionality.

Cheers,
Jan


[1] http://rsb.info.nih.gov/ij/plugins/oval-profile.html




On 28.01.2014, 2:39 PM, Philippe CARL wrote:

> Dear Rick,
> In the case you are interested in the radial profile plugin, I would rather
> recommend you to use my extension version of the plugin:
> http://rsbweb.nih.gov/ij/plugins/radial-profile-ext.html
> which gives you much more features and flexibility (by using the mouse
> and/or keyboard | thanks a lot to Michael Schmid) in order to set the
> position and dimension of the circular ROI.
> Nevertheless what Martin was asking isn't going in the applications of these
> plugins and I think, unless I'm wrong, that his question has been correctly
> answered by Jan...
> My best regards,
> Philippe
>
> -----Message d'origine-----
> De : ImageJ Interest Group [mailto:[hidden email]] De la part de
> Frederic V. Hessman
> Envoyé : mardi 28 janvier 2014 14:11
> À : [hidden email]
> Objet : Re: Annular ROI and profile plot
>
> Martin,
>
> Before asking the net or re-inventing the wheel, you should always look at
> the list of standard external plugins first:
>
> http://rsb.info.nih.gov/ij/plugins/index.html
>
> There are various “radial profile plot” options.  We also have one in the
> astronomy plugins.
>
> Rick
>
> On 28 Jan 2014, at 13:07, MartinG <[hidden email]>
> wrote:
>
>> Thanks for the answer.
>>
>> Unfortunately I want to get a different kind of information (a
>> intensity distribution).
>> A similar profile can achived by using "segemented line slection",
>> setting the "line width" to a certain amount, draw a shape around the
>> desired area and plot profile afterwards.
>> Now I want to get something like that, but with a annual ROI instead
>> of a lot of lines.
>>
>> Martin
>>

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

[MartinG]

Dear All,

than you very much for your help and all the great ideas.

Actually Jans way is exactely what I´ve been locking for:
an Intensity vs. Angle plot arrising from a circular shaped origin.

I have just one question left: Is the intensity value the average intensity of the annular region or the sum of all the values regarding a specific angle?

Thanks a lot.

Martin