sum every x slice of a stack

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sum every x slice of a stack

dschones
Dear All,

I use SEM to take videos of a transistor biased with a triangle voltage (AC)
between emitter and base in order to compare contrast and bias voltage. I
use stacks to manipulate the videos. The video is T periods long. What I
want to do is averaging every x-slice in order to reduce noise.

Lets say I take a video of 3 periods and 360 frames at 10fps. So I want to
average slice 1+121+242, 2+122+243,...120+240+360 and put them together as a
stack of 120 slices.

I thought of first creating substacks to sort the slices like:

for (i=0;i<nSlices;i++) {

run("Make Substack...", "  slices=[i-360-120]");

}

and after combining them using the z-projection tool

run("Z Project...", "start=i stop=i+3 projection=[Average Intensity]");

I'm not so much in programming macros yet. How can I combine them together?

Thanks for helping me.

Best wishes. Jonas



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Re: sum every x slice of a stack

Herbie
Good day Jonas,

as far as I understand, you are working towards your thesis and what you are
asking for since months are to become parts of it. So why not learn to do it
yourself, because it is *your* thesis.

I would use "Paste Control...". Copy and add the desired slices and, after
you've added the desired number of slices, divide the sum by the number of
added slices. You can delete the slices that aren't necessary anymore.

HTH

Herbie

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

Dear All,

I use SEM to take videos of a transistor biased with a triangle voltage (AC)
between emitter and base in order to compare contrast and bias voltage. I
use stacks to manipulate the videos. The video is T periods long. What I
want to do is averaging every x-slice in order to reduce noise.

Lets say I take a video of 3 periods and 360 frames at 10fps. So I want to
average slice 1+121+242, 2+122+243,...120+240+360 and put them together as a
stack of 120 slices.

I thought of first creating substacks to sort the slices like:

for (i=0;i<nSlices;i++) {

run(&quot;Make Substack...&quot;, &quot;  slices=[i-360-120]&quot;);

}

and after combining them using the z-projection tool

run(&quot;Z Project...&quot;, &quot;start=i stop=i+3 projection=[Average
Intensity]&quot;);

I'm not so much in programming macros yet. How can I combine them together?

Thanks for helping me.

Best wishes. Jonas



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Re: sum every x slice of a stack

Fred Damen
In reply to this post by dschones
Greetings,

Convert to a hyper stack such that the slices that you want to average are
successive frames.  Then use F Projector:
http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:frame_projector:start

No programming necessary.

Enjoy,

Fred

On Sat, June 30, 2018 10:22 am, dschones wrote:

> Dear All,
>
> I use SEM to take videos of a transistor biased with a triangle voltage (AC)
> between emitter and base in order to compare contrast and bias voltage. I
> use stacks to manipulate the videos. The video is T periods long. What I
> want to do is averaging every x-slice in order to reduce noise.
>
> Lets say I take a video of 3 periods and 360 frames at 10fps. So I want to
> average slice 1+121+242, 2+122+243,...120+240+360 and put them together as a
> stack of 120 slices.
>
> I thought of first creating substacks to sort the slices like:
>
> for (i=0;i<nSlices;i++) {
>
> run("Make Substack...", "  slices=[i-360-120]");
>
> }
>
> and after combining them using the z-projection tool
>
> run("Z Project...", "start=i stop=i+3 projection=[Average Intensity]");
>
> I'm not so much in programming macros yet. How can I combine them together?
>
> Thanks for helping me.
>
> Best wishes. Jonas
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: sum every x slice of a stack

Herbie
In reply to this post by dschones
Things are much easier than previously thought...

Make n substacks from your sequence and add them by using the Image
Calculator.
(n: number of stacks, i.s. periods)

That's it!

Regards

Herbie

:::::::::::::::::::::::::::::::::::::
Good day Jonas,

as far as I understand, you are working towards your thesis and what you are
asking for since months are to become parts of it. So why not learn to do it
yourself, because it is *your* thesis.

I would use "Paste Control...". Copy and add the desired slices and, after
you've added the desired number of slices, divide the sum by the number of
added slices. You can delete the slices that aren't necessary anymore.

HTH

Herbie

:::::::::::::::::::::::::::::::::::::
Dear All,

I use SEM to take videos of a transistor biased with a triangle voltage (AC)
between emitter and base in order to compare contrast and bias voltage. I
use stacks to manipulate the videos. The video is T periods long. What I
want to do is averaging every x-slice in order to reduce noise.

Lets say I take a video of 3 periods and 360 frames at 10fps. So I want to
average slice 1+121+242, 2+122+243,...120+240+360 and put them together as a
stack of 120 slices.

I thought of first creating substacks to sort the slices like:

for (i=0;i<nSlices;i++) {

run(&quot;Make Substack...&quot;, &quot;  slices=[i-360-120]&quot;);

}

and after combining them using the z-projection tool
run(&quot;Z Project...&quot;, &quot;start=i stop=i+3 projection=[Average
Intensity]&quot;);

I'm not so much in programming macros yet. How can I combine them together?

Thanks for helping me.

Best wishes. Jonas



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Re: sum every x slice of a stack

dschones
Thanks Herbie, Thanks Fred,

I found a similiar solution as Herbies. I convert into n substacks, use
concatenated to recombine and use stack sorter to put in the right order. I
will try the other solutions u posted. Thanks again :)

Have a nice evening, best wishes, Jonas



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Re: sum every x slice of a stack

dschones
dschones wrote
> I convert into n substacks, use concatenated to recombine and use stack
> sorter to put in the right order.

something was missing.. after I use the grouped z-project to average them
best wishes, jonas




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