Open every nth image in a stack?

[Michael Herron]

I am generating very large stacks and it would often be useful when  
importing a stack of images to only open a subset of the stack.  Such  
as the first 100 slices or every third slice.  Is there a way to do  
this?

Thanks,
Mike

[Chrissy-4]

I'm working also with large stacks. If you  import them  the window will
appear where you can type in your starting picture and the increment (it
is normally set up for 1). If you increase your increment now every 2nd
or 3rd picture will be open.
If you want to open the 100 first pics there is only one way which I
know, copy them in a new folder and import them again.

Bye,
Chrissy

Michael J. Herron wrote:

> I am generating very large stacks and it would often be useful when  
> importing a stack of images to only open a subset of the stack.  Such  
> as the first 100 slices or every third slice.  Is there a way to do  
> this?
>
> Thanks,
> Mike
>
>

[Paolo Ariano]

Michael J. Herron ha scritto:
> as the first 100 slices or every third slice.  Is there a way to do  this?

i think the menu of "import stack" is right to do this, you
can choose the last slice (100h) and the shift between
slices (1:3), there are also plug plugins to make tricky
jobs on stacks, see the plugins page ;)

good luck
paolo

--
Paolo Ariano
Neuroscience PhD @ UniTo

[Michael Herron]

Oh that's right, I lost track of that feature.  Thanks.


On Nov 21, 2005, at 7:13 PM, Chrissy wrote:

> I'm working also with large stacks. If you  import them  the window
> will appear where you can type in your starting picture and the
> increment (it is normally set up for 1). If you increase your
> increment now every 2nd or 3rd picture will be open.
> If you want to open the 100 first pics there is only one way which I
> know, copy them in a new folder and import them again.
>
> Bye,
> Chrissy
>
> Michael J. Herron wrote:
>
>> I am generating very large stacks and it would often be useful when  
>> importing a stack of images to only open a subset of the stack.  Such
>>  as the first 100 slices or every third slice.  Is there a way to do  
>> this?
>>
>> Thanks,
>> Mike
>>
>>
>
>

Michael J. Herron,  U of MN, Dept. of Entomology
   [hidden email]
      612-624-3688 (office) 612-625-5299 (FAX)

[Michael Herron]

I think you are referring to Import_> Image Sequence?  This allows me  
to import a sequence of image files but what I am faced with is a  
large TIF stack. I was wondering if it was possible to open or import  
a subset of that large file.


On Nov 21, 2005, at 7:13 PM, Chrissy wrote:

> I'm working also with large stacks. If you  import them  the window  
> will appear where you can type in your starting picture and the  
> increment (it is normally set up for 1). If you increase your  
> increment now every 2nd or 3rd picture will be open.
> If you want to open the 100 first pics there is only one way which  
> I know, copy them in a new folder and import them again.
>
> Bye,
> Chrissy
>
> Michael J. Herron wrote:
>
>> I am generating very large stacks and it would often be useful  
>> when  importing a stack of images to only open a subset of the  
>> stack.  Such  as the first 100 slices or every third slice.  Is  
>> there a way to do  this?
>>
>> Thanks,
>> Mike
>>
>>
>

[Joel Sheffield]

You might be able to use the virtual stack opener to open the whole
stack, which will share memory with the hard drive, and then use the
stacks plugin "slice remover" to eliminate those images you don't
want.

It's a bit kludgey (sp?), but it should work.

Joel

> I think you are referring to Import_> Image Sequence?  This allows me
> to import a sequence of image files but what I am faced with is a
> large TIF stack. I was wondering if it was possible to open or import
> a subset of that large file.
>
>
> On Nov 21, 2005, at 7:13 PM, Chrissy wrote:
>
> > I'm working also with large stacks. If you  import them  the window
> > will appear where you can type in your starting picture and the
> > increment (it is normally set up for 1). If you increase your
> > increment now every 2nd or 3rd picture will be open. If you want to
> > open the 100 first pics there is only one way which  I know, copy
> > them in a new folder and import them again.
> >
> > Bye,
> > Chrissy
> >
> > Michael J. Herron wrote:
> >
> >> I am generating very large stacks and it would often be useful
> >> when  importing a stack of images to only open a subset of the
> >> stack.  Such  as the first 100 slices or every third slice.  Is
> >> there a way to do  this?
> >>
> >> Thanks,
> >> Mike
> >>
> >>
> >

Joel B. Sheffield, Ph.D.
Biology Department, Temple University
1900 North 12th Street
Philadelphia, PA 19122
[hidden email]  
[phone], fax [phone]
http://astro.temple.edu/~jbs

[Wayne Rasband]

>  I am generating very large stacks and it would often be useful 
>  when  importing a stack of images to only open a subset of
>  the stack.  Such  as the first 100 slices or every third slice. 
>  Is there a way to do  this?

You may be able to do this using the File>Import>Raw command if the
images are uncompressed TIFFs, you know the offset to the first image,
and the images are stored consecutively. For example, you can import
the first 10 slices of a 100 slice stack of 512x512 16-bit images using
the macro

   run("Raw...", "width=512 height=512 offset=768 number=10 gap=0")

You can import every third slice using the macro

   run("Raw...", "width=512 height=512 offset=768 number=33 gap=1048576")

These macros assumes the TIFF stack was created by ImageJ, where the
offset to the start of the image data is always 768. To import every
third slice the gap must be set to 512*512*2*2 (1048576).

-wayne

[Michael Herron]

How do I find the offset in a tiff stack?

On Nov 22, 2005, at 10:44 AM, Wayne Rasband wrote:

>>  I am generating very large stacks and it would often be useful
>>  when  importing a stack of images to only open a subset of
>>  the stack.  Such  as the first 100 slices or every third slice.
>>  Is there a way to do  this?
>
> You may be able to do this using the File>Import>Raw command if the  
> images are uncompressed TIFFs, you know the offset to the first  
> image, and the images are stored consecutively. For example, you  
> can import the first 10 slices of a 100 slice stack of 512x512 16-
> bit images using the macro
>
>   run("Raw...", "width=512 height=512 offset=768 number=10 gap=0")
>
> You can import every third slice using the macro
>
>   run("Raw...", "width=512 height=512 offset=768 number=33  
> gap=1048576")
>
> These macros assumes the TIFF stack was created by ImageJ, where  
> the offset to the start of the image data is always 768. To import  
> every third slice the gap must be set to 512*512*2*2 (1048576).
>
> -wayne
>

[Wayne Rasband]

> How do I find the offset in a tiff stack?

It is the value of tag 273 (StripOffsets), which you find by opening
the stack in ImageJ with "Debug Mode" checked in Edit>Options>Misc.

-wayne

> On Nov 22, 2005, at 10:44 AM, Wayne Rasband wrote:
>
> >>  I am generating very large stacks and it would often be useful
> >>  when  importing a stack of images to only open a subset of
> >>  the stack.  Such  as the first 100 slices or every third slice.
> >>  Is there a way to do  this?
> >
> > You may be able to do this using the File>Import>Raw command if the 
> > images are uncompressed TIFFs, you know the offset to the first 
> > image, and the images are stored consecutively. For example, you 
> > can import the first 10 slices of a 100 slice stack of 512x512 16-
> > bit images using the macro
> >
> >   run("Raw...", "width=512 height=512 offset=768 number=10 gap=0")
> >
> > You can import every third slice using the macro
> >
> >   run("Raw...", "width=512 height=512 offset=768 number=33 
> > gap=1048576")
> >
> > These macros assumes the TIFF stack was created by ImageJ, where 
> > the offset to the start of the image data is always 768. To import 
> > every third slice the gap must be set to 512*512*2*2 (1048576).
> >
> > -wayne
> >

[Ye Chen]

Hello,

Current Plugin for opening LSM image
http://rsb.info.nih.gov/ij/plugins/lsm-reader.html LSM-Reader doesn't work
for Zeiss Confocal LSM 510 version 3.5 sp 1.1. Is there anyone knowing
any  plugin which can open LSM images created from Zeiss Confcal LSM510
version 3.5 sp 1.1?

I very appreciate if the developing group for LSM-reader can upgrade this
plugin quickly in order to handle LSM images for all versions of Zeiss
Confocal LSM 510, especially the newest version 3.5 sp1.1.

Thanks

[Michael Herron]

Wayne,

Ok...so I ran ImageJ in the Debug mode and got:

     273, "StripOffsets", value=100600808, count=126

I used 126 in the macro using my image's height and width like this

run("Raw...", "width=1004 height=1002 offset=126 number=10 gap=0")

BUT the images were shifted to the right a bit.
So I tried to decrease the offset and that seemed to help, but on a  
whim I used your example offset of 768 and "wallah" it worked fine.

WHY?

Mike



On Nov 22, 2005, at 12:04 PM, Wayne Rasband wrote:

>> How do I find the offset in a tiff stack?
>
> It is the value of tag 273 (StripOffsets), which you find by  
> opening the stack in ImageJ with "Debug Mode" checked in  
> Edit>Options>Misc.
>
> -wayne
>
>
>> On Nov 22, 2005, at 10:44 AM, Wayne Rasband wrote:
>>
>> >>  I am generating very large stacks and it would often be useful
>> >>  when  importing a stack of images to only open a subset of
>> >>  the stack.  Such  as the first 100 slices or every third slice.
>> >>  Is there a way to do  this?
>> >
>> > You may be able to do this using the File>Import>Raw command if the
>> > images are uncompressed TIFFs, you know the offset to the first
>> > image, and the images are stored consecutively. For example, you
>> > can import the first 10 slices of a 100 slice stack of 512x512 16-
>> > bit images using the macro
>> >
>> >   run("Raw...", "width=512 height=512 offset=768 number=10 gap=0")
>> >
>> > You can import every third slice using the macro
>> >
>> >   run("Raw...", "width=512 height=512 offset=768 number=33
>> > gap=1048576")
>> >
>> > These macros assumes the TIFF stack was created by ImageJ, where
>> > the offset to the start of the image data is always 768. To import
>> > every third slice the gap must be set to 512*512*2*2 (1048576).
>> >
>> > -wayne
>> >
>

[Jerome Mutterer]

Dear all,
Patrick is currently building a new version of the LSM Reader plugin
that will handle files acquired with version 3.5 of the Zeiss software.
Some more testing is required, but a message will be posted to the list
when the new version is available.

Jerome.



Selon Ye Chen <[hidden email]>:

> Hello,
>
> Current Plugin for opening LSM image
> http://rsb.info.nih.gov/ij/plugins/lsm-reader.html LSM-Reader doesn't
> work
> for Zeiss Confocal LSM 510 version 3.5 sp 1.1. Is there anyone
> knowing
> any  plugin which can open LSM images created from Zeiss Confcal
> LSM510
> version 3.5 sp 1.1?
>
> I very appreciate if the developing group for LSM-reader can upgrade
> this
> plugin quickly in order to handle LSM images for all versions of
> Zeiss
> Confocal LSM 510, especially the newest version 3.5 sp1.1.
>
> Thanks
>

--

[Adam Hacking]

Dear List,
 
  Does anyone know if a plugin exists for opening WYKO .opd files with Image J ?
 
  Thanks
 
  Adam Hacking