Timelapse of orthogonal sections

[Carlos Sanchez-8]

Hello, good morning.

 

                Is there an easy way to make a timelapse stack of orthogonal
sections (no projections) from a timelapse satck with slices? Just to show a
change of one XZ or YZ section along the time.

 

Thank you very much for your help.

 

Regards,

 

Carlos Sánchez Martín

Servicio de Microscopía Optica y Confocal (Lab.310)

Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM)

C/Nicolás Cabrera,1

Universidad Autónoma de Madrid. Cantoblanco.

28049. Madrid

Tlfs. 91 196 4613/4643

Fax. [phone]

E-mail: [hidden email]

Web:  <http://www.cbm.uam.es/confocal> http://www.cbm.uam.es/confocal

[Michael Schmid]

Hi Carlos,

is it simply Image/Stacks/Reslice what you want?

Michael
________________________________________________________________

On 6 Mar 2008, at 14:01, Carlos Sanchez wrote:

> Hello, good morning.
>
>                 Is there an easy way to make a timelapse stack of
> orthogonal sections (no projections) from a timelapse satck with
> slices? Just to show a change of one XZ or YZ section along the time.
>
> Thank you very much for your help.
>
> Regards,
>
> Carlos Sánchez Martín
>

[Carlos Sanchez-8]

Thank you very much, Michael.

        What I am looking for is a way to avoid making orthogonal sections
one by one from each timepoint stack of slices (".stk" or ".tiff" formats)
to create then the timelapse stack of that particular orthogonal section.

Regards,

Carlos Sánchez Martín
Servicio de Microscopía Optica y Confocal (Lab.310)
Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM)
C/Nicolás Cabrera,1
Universidad Autónoma de Madrid. Cantoblanco.
28049. Madrid
Tlfs. 91 196 4613/4643
Fax. [phone]
E-mail: [hidden email]
Web: http://www.cbm.uam.es/confocal

[Michael Schmid]

Hi Carlos,

sorry, I don't understand it.

Let us assume your stack is a cube, with image 1 at the bottom
and image nSlices at the top. Let us name the frame number "z
coordinate".
Reslice will cut the cube parallel to the side faces, i.e.
orthogonal to the original image plane, and create a stack of
these images.
You can have the new images in the x or y plane (orthogonal to
each other).

You can play the new stack as time-lapse sequence (Image/StackS/
Start Animation)

What is it that you want in contrast to this?

Michael
________________________________________________________________

On 6 Mar 2008, at 14:56, Carlos Sanchez wrote:

> Thank you very much, Michael.
>
> What I am looking for is a way to avoid making orthogonal sections
> one by one from each timepoint stack of slices (".stk" or ".tiff"  
> formats)
> to create then the timelapse stack of that particular orthogonal  
> section.
>
> Regards,
>
> Carlos Sánchez Martín
> Servicio de Microscopía Optica y Confocal (Lab.310)
> Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM)
> C/Nicolás Cabrera,1
> Universidad Autónoma de Madrid. Cantoblanco.
> 28049. Madrid
> Tlfs. 91 196 4613/4643
> Fax. [phone]
> E-mail: [hidden email]
> Web: http://www.cbm.uam.es/confocal

[Michael Weber-4]

Carlos,

I am not aware of a build-in feature in ImageJ that can produce
orthogonal time-series. One might think about a macro that combines
OrtView or Reslice over time.

However, you can do it in Bitplane Imaris, if you don't have a license
you can request a demo. Improvision Volocity can also do it, and I am
pretty sure it also works in the LE for free.

Michael


Carlos Sanchez wrote:

> Hello, good morning.
>
>  
>
>                 Is there an easy way to make a timelapse stack of orthogonal
> sections (no projections) from a timelapse satck with slices? Just to show a
> change of one XZ or YZ section along the time.
>
>  
>
> Thank you very much for your help.
>
>  
>
> Regards,
>
>  
>
> Carlos Sánchez Martín
>
> Servicio de Microscopía Optica y Confocal (Lab.310)
>
> Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM)
>
> C/Nicolás Cabrera,1
>
> Universidad Autónoma de Madrid. Cantoblanco.
>
> 28049. Madrid
>
> Tlfs. 91 196 4613/4643
>
> Fax. [phone]
>
> E-mail: [hidden email]
>
> Web:  <http://www.cbm.uam.es/confocal> http://www.cbm.uam.es/confocal

[Carlos Sanchez-8]

Thank you very much, Michael

        We are trying with Variables in Metamorph but we thought it might be
an easier way to do it in ImageJ.

Thank you everybody.

Carlos Sánchez Martín
Servicio de Microscopía Optica y Confocal (Lab.310)
Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM)
C/Nicolás Cabrera,1
Universidad Autónoma de Madrid. Cantoblanco.
28049. Madrid
Tlfs. 91 196 4613/4643
Fax. [phone]
E-mail: [hidden email]
Web: http://www.cbm.uam.es/confocal

[Thomas Boudier]

Hi,

I've written a small plugin to do that, it works with lif files (from
leica confocal) but can be adapted to any format. Contact me if you are
interested.

Thomas


Michael Weber a écrit :

> Carlos,
>
> I am not aware of a build-in feature in ImageJ that can produce
> orthogonal time-series. One might think about a macro that combines
> OrtView or Reslice over time.
>
> However, you can do it in Bitplane Imaris, if you don't have a license
> you can request a demo. Improvision Volocity can also do it, and I am
> pretty sure it also works in the LE for free.
>
> Michael
>
>
> Carlos Sanchez wrote:
>> Hello, good morning.
>>
>>  
>>
>>                 Is there an easy way to make a timelapse stack of
>> orthogonal
>> sections (no projections) from a timelapse satck with slices? Just to
>> show a
>> change of one XZ or YZ section along the time.
>>
>>  
>>
>> Thank you very much for your help.
>>
>>  
>>
>> Regards,
>>
>>  
>>
>> Carlos Sánchez Martín
>>
>> Servicio de Microscopía Optica y Confocal (Lab.310)
>>
>> Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM)
>>
>> C/Nicolás Cabrera,1
>>
>> Universidad Autónoma de Madrid. Cantoblanco.
>>
>> 28049. Madrid
>>
>> Tlfs. 91 196 4613/4643
>>
>> Fax. [phone]
>>
>> E-mail: [hidden email]
>>
>> Web:  <http://www.cbm.uam.es/confocal> http://www.cbm.uam.es/confocal
>
>

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