linking and simultaneous viewing of two stacks

[froteros froteros]

Hi,

I wanted to know whether there is a way to link and simultaneously view two
stacks ( channel A and channel B) on ImageJ. I know that if they were on
the same plane I can use Stacks->Tools->Combine, but the problem is in my
case the stacks are in the orthogonal directions. Specifically:

Stack 1: xz stack of 500 frames (t) with each frame is 200x300(x-z).
Stack 2: xt stack of 300 frames (z) with each frame is 200x500 (x-t)

I want to simultaneously view Stack 1 and Stack 2 in a linked manner  For
instance if I click at z = 100 in Stack 1 I want Stack 2 to show frame 100.
Similarly if I click t = 100 is Stack 2 I want Stack 1 to show frame 100.

So. what I want is very similar to the operation of Orthogonal Views, but I
want Stack 2 to be the main view while Stack 1 the XZ view.

Let me know if there is a way to do this via current plugins or some macros.

 Thanks a lot for the help!

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[Rasband, Wayne (NIH/NIMH) [E]]

On Feb 23, 2015, at 6:57 PM, froteros froteros <[hidden email]> wrote:

>
> Hi,
>
> I wanted to know whether there is a way to link and simultaneously view two
> stacks ( channel A and channel B) on ImageJ. I know that if they were on
> the same plane I can use Stacks->Tools->Combine, but the problem is in my
> case the stacks are in the orthogonal directions. Specifically:
>
> Stack 1: xz stack of 500 frames (t) with each frame is 200x300(x-z).
> Stack 2: xt stack of 300 frames (z) with each frame is 200x500 (x-t)
>
> I want to simultaneously view Stack 1 and Stack 2 in a linked manner  For
> instance if I click at z = 100 in Stack 1 I want Stack 2 to show frame 100.
> Similarly if I click t = 100 is Stack 2 I want Stack 1 to show frame 100.
>
> So. what I want is very similar to the operation of Orthogonal Views, but I
> want Stack 2 to be the main view while Stack 1 the XZ view.
>
> Let me know if there is a way to do this via current plugins or some macros.

Try the Analyze>Tools>Synchronize Windows command.

-wayne

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[froteros froteros]

thanks a lot for the reply. Synchronize Windows command works fine if the two stacks were on the same plane (i.e. both are xz stacks), but in my case it doesn't quite work since they are orthogonal. when I load both stacks and synchronize them what happens is that when I scroll to frame 20 in Stack 1 then Stack 2 also goes to fame 20.

But I want to click to the position of z=20 at a frame in Stack 1, which then makes Stack 2 to go frame 20. When I scroll to a different frame in Stack 1, the frame of Stack 2 shouldn't change. This is similar to the how the main and XZ views would behave if I opened Stack 1 and created Orthogonal Views.  I couldn't figure out how to do this operation with Synchronize Windows commands.

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