3D Fourier Transform

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3D Fourier Transform

cromatina
Hi, guys!

I have a stack from a tomographic reconstruction that shows a big structure
made of thin tubes/lines. These lines are present in all the structure, so
I am wondering if it is possible to obtain a 3D Fourier Transform of the
volume to see if there is some distance repetition.

I have been making some tests, but what I have obtained is also a stack. It
seems to be the 1D FT of each slice...and I was expecting a single image.
Am I wrong? When you apply FT to a stack you also obtain a stack? If not,
please help me to find the way!

Thanks in advance!

Andrea

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Re: 3D Fourier Transform

Herbie
Well Andrea,

what you actually get is a "2D FT of every slice" because ImageJ comes
with 2D-FFT only, but there is the ImageJ PlugIn "FFTJ" that performs 3D
FFTs.

Why not have a look at the ImageJ PlugIn page?

Here you are:
<http://rsb.info.nih.gov/ij/plugins/fftj.html>
and don' forget to read
<http://rsb.info.nih.gov/ij/plugins/fftj2.html>

Be aware that you use a power of two sized dimensions of your stack,
otherwise the DFT applies and that will take longer to compute!

HTH

Herbie

::::::::::::::::::::::::::::::::::::::::::::
Am 23.07.15 um 16:32 schrieb Andrea Chicano:

> Hi, guys!
>
> I have a stack from a tomographic reconstruction that shows a big structure
> made of thin tubes/lines. These lines are present in all the structure, so
> I am wondering if it is possible to obtain a 3D Fourier Transform of the
> volume to see if there is some distance repetition.
>
> I have been making some tests, but what I have obtained is also a stack. It
> seems to be the 1D FT of each slice...and I was expecting a single image.
> Am I wrong? When you apply FT to a stack you also obtain a stack? If not,
> please help me to find the way!
>
> Thanks in advance!
>
> Andrea
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: 3D Fourier Transform

Thomas Boudier-3
In reply to this post by cromatina
Hi Andrea,

For a 3D version of FFT, have a look to P. Wendykier work :

https://sites.google.com/site/piotrwendykier/software/parallelfftj

Best,

Thomas


On 23/07/15 22:32, Andrea Chicano wrote:

> Hi, guys!
>
> I have a stack from a tomographic reconstruction that shows a big structure
> made of thin tubes/lines. These lines are present in all the structure, so
> I am wondering if it is possible to obtain a 3D Fourier Transform of the
> volume to see if there is some distance repetition.
>
> I have been making some tests, but what I have obtained is also a stack. It
> seems to be the 1D FT of each slice...and I was expecting a single image.
> Am I wrong? When you apply FT to a stack you also obtain a stack? If not,
> please help me to find the way!
>
> Thanks in advance!
>
> Andrea
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
   /***************************************************************/
      Thomas Boudier, Associate Professor, UPMC,
      Université Pierre et Marie Curie, Paris, France.
      BioInformatics Institute (BII)/IPAL, Singapore.
/**************************************************************/

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Re: 3D Fourier Transform

cromatina
Hi Thomas,

thank you! This helps a lot! I'll check the work and try to apply to my
samples.

Best,
Andrea

2015-07-24 6:52 GMT+02:00 Thomas Boudier <[hidden email]>:

> Hi Andrea,
>
> For a 3D version of FFT, have a look to P. Wendykier work :
>
> https://sites.google.com/site/piotrwendykier/software/parallelfftj
>
> Best,
>
> Thomas
>
>
>
> On 23/07/15 22:32, Andrea Chicano wrote:
>
>> Hi, guys!
>>
>> I have a stack from a tomographic reconstruction that shows a big
>> structure
>> made of thin tubes/lines. These lines are present in all the structure, so
>> I am wondering if it is possible to obtain a 3D Fourier Transform of the
>> volume to see if there is some distance repetition.
>>
>> I have been making some tests, but what I have obtained is also a stack.
>> It
>> seems to be the 1D FT of each slice...and I was expecting a single image.
>> Am I wrong? When you apply FT to a stack you also obtain a stack? If not,
>> please help me to find the way!
>>
>> Thanks in advance!
>>
>> Andrea
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
>   /***************************************************************/
>      Thomas Boudier, Associate Professor, UPMC,
>      Université Pierre et Marie Curie, Paris, France.
>      BioInformatics Institute (BII)/IPAL, Singapore.
> /**************************************************************/
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: 3D Fourier Transform

Stephan Preibisch
Hi Andrea,

you can also check out ImgLib2: http://fiji.sc/ImgLib2_Examples#Example_6c_-_Complex_numbers_and_Fourier_transforms <http://fiji.sc/ImgLib2_Examples#Example_6c_-_Complex_numbers_and_Fourier_transforms>

It is part of Fiji and can be called through a Beanshell script for example.

Hope this helps,
Stephan

> On Jul 24, 2015, at 10:48 , Andrea Chicano <[hidden email]> wrote:
>
> Hi Thomas,
>
> thank you! This helps a lot! I'll check the work and try to apply to my
> samples.
>
> Best,
> Andrea
>
> 2015-07-24 6:52 GMT+02:00 Thomas Boudier <[hidden email]>:
>
>> Hi Andrea,
>>
>> For a 3D version of FFT, have a look to P. Wendykier work :
>>
>> https://sites.google.com/site/piotrwendykier/software/parallelfftj
>>
>> Best,
>>
>> Thomas
>>
>>
>>
>> On 23/07/15 22:32, Andrea Chicano wrote:
>>
>>> Hi, guys!
>>>
>>> I have a stack from a tomographic reconstruction that shows a big
>>> structure
>>> made of thin tubes/lines. These lines are present in all the structure, so
>>> I am wondering if it is possible to obtain a 3D Fourier Transform of the
>>> volume to see if there is some distance repetition.
>>>
>>> I have been making some tests, but what I have obtained is also a stack.
>>> It
>>> seems to be the 1D FT of each slice...and I was expecting a single image.
>>> Am I wrong? When you apply FT to a stack you also obtain a stack? If not,
>>> please help me to find the way!
>>>
>>> Thanks in advance!
>>>
>>> Andrea
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
>> --
>>  /***************************************************************/
>>     Thomas Boudier, Associate Professor, UPMC,
>>     Université Pierre et Marie Curie, Paris, France.
>>     BioInformatics Institute (BII)/IPAL, Singapore.
>> /**************************************************************/
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html


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Re: 3D Fourier Transform

cromatina
Hi Stephan,

I'll check it! Thank you.

Best,
Andrea



2015-07-24 14:34 GMT+02:00 Stephan Preibisch <[hidden email]>:

> Hi Andrea,
>
> you can also check out ImgLib2:
> http://fiji.sc/ImgLib2_Examples#Example_6c_-_Complex_numbers_and_Fourier_transforms
> <
> http://fiji.sc/ImgLib2_Examples#Example_6c_-_Complex_numbers_and_Fourier_transforms
> >
>
> It is part of Fiji and can be called through a Beanshell script for
> example.
>
> Hope this helps,
> Stephan
>
> > On Jul 24, 2015, at 10:48 , Andrea Chicano <[hidden email]>
> wrote:
> >
> > Hi Thomas,
> >
> > thank you! This helps a lot! I'll check the work and try to apply to my
> > samples.
> >
> > Best,
> > Andrea
> >
> > 2015-07-24 6:52 GMT+02:00 Thomas Boudier <[hidden email]>:
> >
> >> Hi Andrea,
> >>
> >> For a 3D version of FFT, have a look to P. Wendykier work :
> >>
> >> https://sites.google.com/site/piotrwendykier/software/parallelfftj
> >>
> >> Best,
> >>
> >> Thomas
> >>
> >>
> >>
> >> On 23/07/15 22:32, Andrea Chicano wrote:
> >>
> >>> Hi, guys!
> >>>
> >>> I have a stack from a tomographic reconstruction that shows a big
> >>> structure
> >>> made of thin tubes/lines. These lines are present in all the
> structure, so
> >>> I am wondering if it is possible to obtain a 3D Fourier Transform of
> the
> >>> volume to see if there is some distance repetition.
> >>>
> >>> I have been making some tests, but what I have obtained is also a
> stack.
> >>> It
> >>> seems to be the 1D FT of each slice...and I was expecting a single
> image.
> >>> Am I wrong? When you apply FT to a stack you also obtain a stack? If
> not,
> >>> please help me to find the way!
> >>>
> >>> Thanks in advance!
> >>>
> >>> Andrea
> >>>
> >>> --
> >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>>
> >>
> >> --
> >>  /***************************************************************/
> >>     Thomas Boudier, Associate Professor, UPMC,
> >>     Université Pierre et Marie Curie, Paris, France.
> >>     BioInformatics Institute (BII)/IPAL, Singapore.
> >> /**************************************************************/
> >>
> >>
> >> --
> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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