FFT/Inverse FFT of Image Stack

[c8965]

Is there a plugin that can carry out an FFT and inverse FFT of an image stack along the z-axis?

[Cammer, Michael]

You may reslice a stack, FFT filter each slice and paste it back, and then reslice the stack back to the original orientation.  This can be done in a simple loop in a macro.
-Michael C.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of c8965
Sent: Wednesday, April 25, 2012 2:32 PM
To: [hidden email]
Subject: FFT/Inverse FFT of Image Stack

Is there a plugin that can carry out an FFT and inverse FFT of an image stack along the z-axis?

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[Herbie-6]

>Is there a plugin that can carry out an FFT and inverse FFT of an image stack
>along the z-axis?
>
>--
>View this message in context:
>http://imagej.1557.n6.nabble.com/FFT-Inverse-FFT-of-Image-Stack-tp4917583p4917583.html
>Sent from the ImageJ mailing list archive at Nabble.com.

Dear c8965!

An image stack means a volume, so if you want to keep the spatial x-
and y-axes and only Fourier-transform along z, then this means a
great number, namely the number of pixels in the xy-plane, of
one-dimensional Fourier-transformations. However, ImageJ provides
means for two-dimensional Fourier-transformations only.

HTH
--

                   Herbie

          ------------------------
          <http://www.gluender.de>

[Stephan Preibisch]

Hi,

if you know how to program, the 1-d fft implementation by Dave Hale included in Fiji can do exactly that. The jar is called edu_mines_jtk.jar. You will find help here: http://inside.mines.edu/~dhale/jtk/

The FFT part is pure java without native code - and still scaringly fast :) You will have to run it for each z-vector along all x,y coordinates. This can be assembled into a 3-d complex image.

Bye bye,
Stephan



Am Apr 25, 2012 um 14:31 schrieb c8965 <[hidden email]>:

> Is there a plugin that can carry out an FFT and inverse FFT of an image stack
> along the z-axis?
>
> --
> View this message in context: http://imagej.1557.n6.nabble.com/FFT-Inverse-FFT-of-Image-Stack-tp4917583p4917583.html
> Sent from the ImageJ mailing list archive at Nabble.com.

[Unruh, Jay-2]

I have a plugin that does that in my collection at http://research.stowers.org/imagejplugins.  It is under Plugins>ICS Tools>stack temporal fft jru v1.  Note that it will automatically truncate the data at some even length (power of 2 or something similar--see the source code for more details).  It is also quite fast but the speed is dependent on how close your data set is to a power of 2.  It takes ~12 sec for a 256x256x1024 size stack and ~18 sec for the same stack truncated to 960 frames.  The data is output as an interlaced stack (real, imaginary, real, imaginary,...).  You can use my complex amp jru v1 plugin to get the amplitude.

Jay

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of c8965
Sent: Wednesday, April 25, 2012 1:32 PM
To: [hidden email]
Subject: FFT/Inverse FFT of Image Stack

Is there a plugin that can carry out an FFT and inverse FFT of an image stack along the z-axis?

--
View this message in context: http://imagej.1557.n6.nabble.com/FFT-Inverse-FFT-of-Image-Stack-tp4917583p4917583.html
Sent from the ImageJ mailing list archive at Nabble.com.