creating stack containing only odd or even stack

[srai]

Hello everyone

My image stack seems to have alternating high and low level of noise. Therefore I want to analyse the odd and the even numbered stacks individually.

Is there a way I can duplicate only odd or even stacks to create a new image stack?

Thanks
Srai

[Daniel Kalthoff]

Hi Srai,

there might be a simple solution. Let's say your stack has 50 slices.

1. Use Image > Stacks > Make Montage ... with 2 columns and 25 rows
2. Go the other way around with Image > Stacks > Tools > Montage to Stack ... and now use 1 column and 25 rows

The resulting stack will consist of odd images on the left, even images on the right hand side.

3. You can use duplicate and crop to create two separate stacks for both.

Best regards,

Daniel

Am 12.05.2011 um 16:29 schrieb Sahara Rai:

> Hello everyone
>
> My image stack seems to have alternating high and low level of noise. Therefore I want to analyse the odd and the even numbered stacks individually.
>
> Is there a way I can duplicate only odd or even stacks to create a new image stack?
>
> Thanks
> Srai

[John Oreopoulos]

I think you could do the same thing with the hyperstacks tools. Make your stack into a hyperstack using the "t" variable to separate the odd and even slices. Then you can use the reduce dimensionality hyperstacks function to separate into two sub-stacks.

John Oreopoulos

 
On 2011-05-12, at 10:35 AM, Daniel Kalthoff wrote:

> Hi Srai,
>
> there might be a simple solution. Let's say your stack has 50 slices.
>
> 1. Use Image > Stacks > Make Montage ... with 2 columns and 25 rows
> 2. Go the other way around with Image > Stacks > Tools > Montage to Stack ... and now use 1 column and 25 rows
>
> The resulting stack will consist of odd images on the left, even images on the right hand side.
>
> 3. You can use duplicate and crop to create two separate stacks for both.
>
> Best regards,
>
> Daniel
>
> Am 12.05.2011 um 16:29 schrieb Sahara Rai:
>
>> Hello everyone
>>
>> My image stack seems to have alternating high and low level of noise. Therefore I want to analyse the odd and the even numbered stacks individually.
>>
>> Is there a way I can duplicate only odd or even stacks to create a new image stack?
>>
>> Thanks
>> Srai

[jchanson]

        For separating the even and odd images...  If the the original
images are stored as a series of images, you can use the menu File |
Import | Image Sequence to specify which images to load.  Load the data as
2 different sets, the first with a starting image of "1" and an increment
of 2, and the second with a starting image of "2" and an increment of 2.
        In order to get this to work with a TIF stack, I had to first save
the image stack as a series of separate images, using the File | Save As |
Image Sequence command.

Jeff



Sahara Rai <[hidden email]>
Sent by: ImageJ Interest Group <[hidden email]>
05/12/2011 10:29 AM
Please respond to
ImageJ Interest Group <[hidden email]>


To
<[hidden email]>
cc

Subject
creating stack containing only odd or even stack






Hello everyone

My image stack seems to have alternating high and low level of noise.
Therefore I want to analyse the odd and the even numbered stacks
individually.

Is there a way I can duplicate only odd or even stacks to create a new
image stack?

Thanks
Srai

[Daniel Kalthoff]

I agree, John's method is more elegant. Just take care about the order of dimensions in the hyperstack, it must be first frames and then slices.
This macro does the job, I guess:

// -------------------------------------------------------
// separate odd and even slices in a stack

getDimensions(w, h, c, z, t);
run("Stack to Hyperstack...", "order=xyctz channels=1 slices=" + (z/2) + " frames=2 display=Color");
ID = getImageID();

run("Duplicate...", "title=odd duplicate frames=1");

selectImage(ID);
run("Duplicate...", "title=even duplicate frames=2");

// -------------------------------------------------------

Regards,

Daniel

Am 12.05.2011 um 16:56 schrieb John Oreopoulos:

> I think you could do the same thing with the hyperstacks tools. Make your stack into a hyperstack using the "t" variable to separate the odd and even slices. Then you can use the reduce dimensionality hyperstacks function to separate into two sub-stacks.
>
> John Oreopoulos
>
>
> On 2011-05-12, at 10:35 AM, Daniel Kalthoff wrote:
>
>> Hi Srai,
>>
>> there might be a simple solution. Let's say your stack has 50 slices.
>>
>> 1. Use Image > Stacks > Make Montage ... with 2 columns and 25 rows
>> 2. Go the other way around with Image > Stacks > Tools > Montage to Stack ... and now use 1 column and 25 rows
>>
>> The resulting stack will consist of odd images on the left, even images on the right hand side.
>>
>> 3. You can use duplicate and crop to create two separate stacks for both.
>>
>> Best regards,
>>
>> Daniel
>>
>> Am 12.05.2011 um 16:29 schrieb Sahara Rai:
>>
>>> Hello everyone
>>>
>>> My image stack seems to have alternating high and low level of noise. Therefore I want to analyse the odd and the even numbered stacks individually.
>>>
>>> Is there a way I can duplicate only odd or even stacks to create a new image stack?
>>>
>>> Thanks
>>> Srai

[David Strachan]

Hi Srai,

You can achieve your goal simply with the command >Image - Stacks - Tools - make substack ...

Regards

David Strachan
[hidden email]


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Sahara Rai
Sent: 12 May 2011 15:30
To: [hidden email]
Subject: creating stack containing only odd or even stack

Hello everyone

My image stack seems to have alternating high and low level of noise. Therefore I want to analyse the odd and the even numbered stacks individually.

Is there a way I can duplicate only odd or even stacks to create a new image stack?

Thanks
Srai