Circular profiles?

[Stefanie Rosa]

Dear all,

Does anyone know if and how can I do oval/circular profiles on ImageJ?
There's a plugin in called Oval profile plot but that one gives intensity
values along the radius and I would like to get a column average plot
instead...but the plot profile function only allows rectangles and lines...

Thanks in advance,
Stefanie

[Jan Eglinger-5]

Dear Stefanie,

Stefanie Rosa wrote:
> Does anyone know if and how can I do oval/circular profiles on ImageJ?
> There's a plugin in called Oval profile plot but that one gives intensity
> values along the radius and I would like to get a column average plot
> instead...but the plot profile function only allows rectangles and lines...

I can hardly imagine a situation where it is meaningful to plot the
column average of columns of different length...

But, as a (rather cumbersome) workaround, you can use the 3D Project
command to get an average value of your (1-slice) stack along a
specified axis (you have to create a stack first by duplicating your
image in a new slice).
The following macro illustrates this (mind the line breaks introduced by
the mailer):


// Plot profile of an oval ROI via Stack, 3D Project, Line selection
run("Gel (105K)");
run("Select All");
run("Copy");
run("Add Slice");
run("Paste");
makeOval(33, 262, 221, 81);
run("3D Project...", "projection=[Mean Value] axis=X-Axis slice=1
initial=90 total=0 rotation=10 lower=1 upper=255 opacity=0 surface=100
interior=50");
makeLine(0, 41, 220, 41);
run("Plot Profile");


Hope it helps,
Jan

[Michael Schmid]

Hi Stefanie,

what about the polar transformer plugin? It converts circles into a  
straight lines.
   http://rsb.info.nih.gov/ij/plugins/polar-transformer.html

Michael
________________________________________________________________

On 13 Oct 2009, at 18:14, Stefanie Rosa wrote:

> Dear all,
>
> Does anyone know if and how can I do oval/circular profiles on ImageJ?
> There's a plugin in called Oval profile plot but that one gives  
> intensity
> values along the radius and I would like to get a column average plot
> instead...but the plot profile function only allows rectangles and  
> lines...
>
> Thanks in advance,
> Stefanie

[Stefanie Rosa]

Hi Jan!

Well I know it sounds a bit weird but it does make sense for the things I'm
doing...
And your suggestion was very good! Thanks a lot!

Now, one more thing, maybe you can help me...
I'm doing analysis on a stack (time series, 60 time points), which means
every time I have to convert the stack to images and do the analysis for
each image afterward...(and repeat that for 100 nuclei!) Which means a hell
of a lot of work...

Any idea of how to make this more automatic?
Thanks a million,
Stefanie
2009/10/13 Jan Eglinger <[hidden email]>



Dear Stefanie,

>
> Stefanie Rosa wrote:
> > Does anyone know if and how can I do oval/circular profiles on ImageJ?
> > There's a plugin in called Oval profile plot but that one gives intensity
> > values along the radius and I would like to get a column average plot
> > instead...but the plot profile function only allows rectangles and
> lines...
>
> I can hardly imagine a situation where it is meaningful to plot the
> column average of columns of different length...
>
> But, as a (rather cumbersome) workaround, you can use the 3D Project
> command to get an average value of your (1-slice) stack along a
> specified axis (you have to create a stack first by duplicating your
> image in a new slice).
> The following macro illustrates this (mind the line breaks introduced by
> the mailer):
>
>
> // Plot profile of an oval ROI via Stack, 3D Project, Line selection
> run("Gel (105K)");
> run("Select All");
> run("Copy");
> run("Add Slice");
> run("Paste");
> makeOval(33, 262, 221, 81);
> run("3D Project...", "projection=[Mean Value] axis=X-Axis slice=1
> initial=90 total=0 rotation=10 lower=1 upper=255 opacity=0 surface=100
> interior=50");
> makeLine(0, 41, 220, 41);
> run("Plot Profile");
>
>
> Hope it helps,
> Jan
>

[Jan Eglinger-5]

Hi Stefanie,

I'm not sure if I understand your problem correctly. Maybe you have an
example image?

Stefanie Rosa wrote:
> Now, one more thing, maybe you can help me...
> I'm doing analysis on a stack (time series, 60 time points), which means
> every time I have to convert the stack to images and do the analysis for
> each image afterward...(and repeat that for 100 nuclei!) Which means a hell
> of a lot of work...

If you already have a stack, you can possibly omit the copying step and
just plot at the correct height (= previous slice number) after 3D project..

So you're analyzing nuclei.. do you detect them automatically (e.g. by
thresholding)? Then you could add them to the ROI manager via "Analyze
particles" and do the profile plot for each of them using for-loops.

See the macro language reference here:
http://rsbweb.nih.gov/ij/developer/macro/macros.html#loops
Useful example macros are here:
http://rsbweb.nih.gov/ij/macros/examples/

Best,
jan

>
>> Stefanie Rosa wrote:
>>> Does anyone know if and how can I do oval/circular profiles on ImageJ?
>>> There's a plugin in called Oval profile plot but that one gives intensity
>>> values along the radius and I would like to get a column average plot
>>> instead...but the plot profile function only allows rectangles and
>> lines...
>>