Import->Virtual Stack ...

[karo03]

Interesting behavior of "Import -> Virtual Stack..."!
if I select an analyze file *.img or *.hdr the program tries  
seemingly to read in all img files in the folder up to memory  
exhaustion.

I expected that only one slice of the stack is read in? Each of my  
img files contain one 3d stack. Possibly I have misunderstood the  
virtual stack?

Thanks for any hint or help
Karsten

[Wayne Rasband]

The File>Import>Image Sequence command does not work with the  
Analyze_Reader plugin. It does work with reader plugins that extend  
the ImagePlus class, such as IPLab_Reader or Biorad_Reader. In  
addition, the "Use Virtual Stack" option only works with a series of  
individual images, not with stacks.

-wayne

On Sep 4, 2007, at 10:51 AM, Karsten Rodenacker wrote:

> Interesting behavior of "Import -> Virtual Stack..."!
> if I select an analyze file *.img or *.hdr the program tries  
> seemingly to read in all img files in the folder up to memory  
> exhaustion.
>
> I expected that only one slice of the stack is read in? Each of my  
> img files contain one 3d stack. Possibly I have misunderstood the  
> virtual stack?
>
> Thanks for any hint or help
> Karsten

[karo03]

Thank you, Wayne, for the information.

Is there any other possibility to extract from a stack one slice as  
image? I find only "Convert Stack to Images" for all images. In my  
case I have some thousand z (or better t) slices, which causes some  
problems.

Karsten

Am 09.09.2007 um 02:20 schrieb Rasband Wayne:

> The File>Import>Image Sequence command does not work with the  
> Analyze_Reader plugin. It does work with reader plugins that extend  
> the ImagePlus class, such as IPLab_Reader or Biorad_Reader. In  
> addition, the "Use Virtual Stack" option only works with a series  
> of individual images, not with stacks.
>
> -wayne
>
> On Sep 4, 2007, at 10:51 AM, Karsten Rodenacker wrote:
>
>> Interesting behavior of "Import -> Virtual Stack..."!
>> if I select an analyze file *.img or *.hdr the program tries  
>> seemingly to read in all img files in the folder up to memory  
>> exhaustion.
>>
>> I expected that only one slice of the stack is read in? Each of my  
>> img files contain one 3d stack. Possibly I have misunderstood the  
>> virtual stack?
>>
>> Thanks for any hint or help
>> Karsten

[Michael Weber-4]

Hi Karsten,

1) select the plane of interest in the stack
2) image > duplicate

You can also reduce the stack by deleting slices before and after the
current image. Or do this in a certain range and then convert the stack
into images.

cheers,
Michael


Karsten Rodenacker wrote:

> Thank you, Wayne, for the information.
>
> Is there any other possibility to extract from a stack one slice as
> image? I find only "Convert Stack to Images" for all images. In my case
> I have some thousand z (or better t) slices, which causes some problems.
>
> Karsten
>
> Am 09.09.2007 um 02:20 schrieb Rasband Wayne:
>
>> The File>Import>Image Sequence command does not work with the
>> Analyze_Reader plugin. It does work with reader plugins that extend
>> the ImagePlus class, such as IPLab_Reader or Biorad_Reader. In
>> addition, the "Use Virtual Stack" option only works with a series of
>> individual images, not with stacks.
>>
>> -wayne
>>
>> On Sep 4, 2007, at 10:51 AM, Karsten Rodenacker wrote:
>>
>>> Interesting behavior of "Import -> Virtual Stack..."!
>>> if I select an analyze file *.img or *.hdr the program tries
>>> seemingly to read in all img files in the folder up to memory
>>> exhaustion.
>>>
>>> I expected that only one slice of the stack is read in? Each of my
>>> img files contain one 3d stack. Possibly I have misunderstood the
>>> virtual stack?
>>>
>>> Thanks for any hint or help
>>> Karsten

[karo03]

Thank, Michael, you for that hint.
I never tried image related functions on stacks. That eases many things.

Karsten

Am 10.09.2007 um 14:03 schrieb Michael Weber:

> Hi Karsten,
>
> 1) select the plane of interest in the stack
> 2) image > duplicate
>
> You can also reduce the stack by deleting slices before and after  
> the current image. Or do this in a certain range and then convert  
> the stack into images.
>
> cheers,
> Michael
>
>
> Karsten Rodenacker wrote:
>> Thank you, Wayne, for the information.
>> Is there any other possibility to extract from a stack one slice  
>> as image? I find only "Convert Stack to Images" for all images. In  
>> my case I have some thousand z (or better t) slices, which causes  
>> some problems.
>> Karsten
>> Am 09.09.2007 um 02:20 schrieb Rasband Wayne:
>>> The File>Import>Image Sequence command does not work with the  
>>> Analyze_Reader plugin. It does work with reader plugins that  
>>> extend the ImagePlus class, such as IPLab_Reader or  
>>> Biorad_Reader. In addition, the "Use Virtual Stack" option only  
>>> works with a series of individual images, not with stacks.
>>>
>>> -wayne
>>>
>>> On Sep 4, 2007, at 10:51 AM, Karsten Rodenacker wrote:
>>>
>>>> Interesting behavior of "Import -> Virtual Stack..."!
>>>> if I select an analyze file *.img or *.hdr the program tries  
>>>> seemingly to read in all img files in the folder up to memory  
>>>> exhaustion.
>>>>
>>>> I expected that only one slice of the stack is read in? Each of  
>>>> my img files contain one 3d stack. Possibly I have misunderstood  
>>>> the virtual stack?
>>>>
>>>> Thanks for any hint or help
>>>> Karsten