How can I plot line intensity profile over time in imageJ?

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How can I plot line intensity profile over time in imageJ?

anran591223
Hi All,

I'm trying to perform intensity analysis on videos in imageJ. The final goal
is to obtain the line intensities acquired from 'plot profile' over the
entire say 100 frames of the video. I cannot use the time analysis plugin
because it only allows to perform such analysis in ROIs generating averaged
intensity over a selected area...

Thanks



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Re: How can I plot line intensity profile over time in imageJ?

Herbie
What about using the "Live"-mode of Plot Profile?

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::

anran591223 wrote

> Hi All,
>
> I'm trying to perform intensity analysis on videos in imageJ. The final
> goal
> is to obtain the line intensities acquired from 'plot profile' over the
> entire say 100 frames of the video. I cannot use the time analysis plugin
> because it only allows to perform such analysis in ROIs generating
> averaged
> intensity over a selected area...
>
> Thanks
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html





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Re: How can I plot line intensity profile over time in imageJ?

anran591223
Thank you for the reply Herbie. That is actually exactly part of what I
wanted - to have all the data (say the line is 10 pixels and video has 20
frames), i.e., a 20 x 10 (# of frame x pixel) matrix in one file... the
'live' mode will allow to generate 1, i.e., 1x10 so I'm just wondering if
there is a easy way to put them together.

Thanks





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Re: How can I plot line intensity profile over time in imageJ?

Herbie
Good day,

actually I don't really understand what you like to obtain.

The live-mode gives you a temporal view of the line profile, when the
stack is animated.
If you like to get all profile plots in parallel, i.e. not as a temporal
sequence, you need to write a little macro that gives you as many
profile plots as you have slices in your stack.

What do you mean by "the line is 10 pixels"?
10 pixels long or wide?

"matrix in one file"
Does that mean you don't want plots but the gray values along the
selection line?

If the latter is what you want, then here is an ImageJ-macro that shows
how to do that. (It uses a demo stack of 27 slices.)

///////////////////////////////////////////////////////
x=96;   // selection x-start
y=100;  // selection y-position
len=50; // selection length
run("MRI Stack (528K)"); // demo image
setBatchMode(true);
img=getImageID();
makeRectangle(x, y, len, 1);
n=nSlices;
newImage("Result", "8-bit black", len, n, 1);
rslt=getImageID();
for ( i=0; i<n; i++ ) {
    selectImage(img);
    setSlice(i+1);
    run("Copy");
    selectImage(rslt);
    makeRectangle(0, i, len, 1);
    run("Paste");
}
run("Select None");
selectImage(img);
setSlice(1);
selectImage(rslt);
setBatchMode(false);
run("Set... ", "zoom=1600 x=25 y=0 width=50 height=1");
exit();
///////////////////////////////////////////////////////

Paste the above macro code to an empty macro window (Plugins >> New >>
Macro) and run it.
(You need an open internet connection to load the demo stack.)

HTH

Herbie

::::::::::::::::::::::::::::::::::::::::
Am 09.04.19 um 02:00 schrieb anran591223:
> Thank you for the reply Herbie. That is actually exactly part of what I
> wanted - to have all the data (say the line is 10 pixels and video has 20
> frames), i.e., a 20 x 10 (# of frame x pixel) matrix in one file... the
> 'live' mode will allow to generate 1, i.e., 1x10 so I'm just wondering if
> there is a easy way to put them together.
>
> Thanks

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Re: How can I plot line intensity profile over time in imageJ?

Adrian Daerr-2
In reply to this post by anran591223
Hi,
Select your line, then go to Image->Stacks->Reslice.
Then save in the format you want.
HTH
Adrian


On 08/04/2019 17.40, anran591223 wrote:
> I'm trying to perform intensity analysis on videos in imageJ. The final goal
> is to obtain the line intensities acquired from 'plot profile' over the
> entire say 100 frames of the video. I cannot use the time analysis plugin
> because it only allows to perform such analysis in ROIs generating averaged
> intensity over a selected area...

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Re: How can I plot line intensity profile over time in imageJ?

Herbie
Good day Adrian,

your suggestion is highly elegant!

The result is in fact identical to what my lengthy macro produces...

Thanks

Herbie

::::::::::::::::::::::::::::::::::::::::::
Am 09.04.19 um 12:49 schrieb Adrian Daerr:

> Hi,
> Select your line, then go to Image->Stacks->Reslice.
> Then save in the format you want.
> HTH
> Adrian
>
>
> On 08/04/2019 17.40, anran591223 wrote:
>> I'm trying to perform intensity analysis on videos in imageJ. The
>> final goal
>> is to obtain the line intensities acquired from 'plot profile' over the
>> entire say 100 frames of the video. I cannot use the time analysis plugin
>> because it only allows to perform such analysis in ROIs generating
>> averaged
>> intensity over a selected area...

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