Plot profile over time

[PabloSAguilar]

Hi there,
I acquire stack of images along time of cells with cytoplasmic GFP,
drawing a 5-pixels wide line within a cell I want to get all the intensity profiles of that line (distance vs. gray value) over time
how can I do that?
It is similar to using the "Live" button of the Analysis/Plot Profile tool while sliding the time stacks, but instead of seeing the profiles flying over time, I want to get the numbers for each profile.
 
Thanks!
Pablo
 

[C Heeney]

Pablo,

It's not clear from your post whether you've tried anything in particular, so here is a very basic way to do what you're thinking of (makes the assumption that the position of the cell you're interested in doesn't move in the image).

1) Make a point selection on any image in the stack (the point should be on the "line" you would draw).
[don't try using the line selection, it won't work for this]

2) Image -> Stacks -> Plot Z-axis Profile

3) The results and the profile are the point selection projected through time. Save to a file / paste into excel / other

4) move the point selection to the next part of the line and repeat steps 1-3.


Here's an alternative that only works if your line selection would be purely horizontal or vertical

1) Generate Orthogonal views:  (Image -> Stacks -> Orthogonal Views)
2) Move the slice markers so that they cut through the area you're interested in
3) If your line is horizontal then duplicate the XZ image.
3a) If your line is vertical, then duplicate the YZ image.

4) Close the orthogonal views and measure intensity profiles in the duplicated image as you require.


Finally, you could also check out the View5D applet (Image -> Stacks -> View5D). There's a bit of learning associated with it, so visit the authors page at   http://nanoimaging.de/view5d 


Cheers

> Hi there,
> I acquire stack of images along time of cells with cytoplasmic GFP,
> drawing a 5-pixels wide line within a cell I want to get all the intensity
> profiles of that line (distance vs. gray value) over time
> how can I do that?
> It is similar to using the "Live" button of the Analysis/Plot Profile tool
> while sliding the time stacks, but instead of seeing the profiles flying
> over time, I want to get the numbers for each profile.
 
> Thanks!
> Pablo

 

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[Michael Entrup]

Hi Pablo,

I provide you a basic example on how to use a macro to perform the task:

run("MRI Stack (528K)");
makeLine(50, 100, 150, 100);
N = nSlices;
array = -1;
for (i=1; i<=N; i++) {
     setSlice(i);
     if (array == -1) {
         array = getProfile();
     } else {
         // Using getProfile() as an argument of Array.concat() does not
work that is why I use nextProfile array.
         nextProfile = getProfile();
         array = Array.concat(array, nextProfile);
     }
}
Array.show("Values", array);
close();

At [1] you can find all available macro functions, to enhance the
example to fulfil your needs.

Best regards
Michael

[1] http://rsbweb.nih.gov/ij/developer/macro/functions.html


Am 17.01.2014 03:08, schrieb PabloSAguilar:

> Hi there,
> I acquire stack of images along time of cells with cytoplasmic GFP,
> drawing a 5-pixels wide line within a cell I want to get all the intensity
> profiles of that line (distance vs. gray value) over time
> how can I do that?
> It is similar to using the "Live" button of the Analysis/Plot Profile tool
> while sliding the time stacks, but instead of seeing the profiles flying
> over time, I want to get the numbers for each profile.
>
> Thanks!
> Pablo
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Plot-profile-over-time-tp5006147.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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ImageJ mailing list: http://imagej.nih.gov/ij/list.html