Image Registration

[JimmiB]

I am looking for a simple way to measure the transformation
required to achieve proper image registration between a set of
reference images and then to apply this same transformation to a
stack.
I have been able to achieve fantastic results with bUnwarpJ on
the reference image, but cannot work out how to apply this to
other images.
MultiStackReg works well on some data sets, but ideally i would
like to apply exactly the same transformation to every image.
Cheers,
James

[Stephan Saalfeld]

Check the Fiji plugins

Register Virtual Stack Slices

http://pacific.mpi-cbg.de/wiki/index.php/Register_Virtual_Stack_Slices

and

Transform Virtual Stack Slices

http://pacific.mpi-cbg.de/wiki/index.php/Transform_Virtual_Stack_Slices

they incorporate bUnwarpJ, feature based registration and allow you to
save the estimated transformation and apply it to other images later.

Good luck,
Stephan


On Wed, 2010-12-15 at 11:24 +1100, James Burchfield wrote:

> I am looking for a simple way to measure the transformation
> required to achieve proper image registration between a set of
> reference images and then to apply this same transformation to a
> stack.
> I have been able to achieve fantastic results with bUnwarpJ on
> the reference image, but cannot work out how to apply this to
> other images.
> MultiStackReg works well on some data sets, but ideally i would
> like to apply exactly the same transformation to every image.
> Cheers,
> James

[JimmiB]

Thanks Stephan,
I have already played with these plugins but cannot get them
to do what i want.  The Transform Virtual Stack Slices plugin
appears to require a separate transformation file for every
image,  what i want to do is apply a single transformation to
multiple images.  Is this possible with those plugins?
James

>
>Check the Fiji plugins
>
>Register Virtual Stack Slices
>
>http://pacific.mpi-
cbg.de/wiki/index.php/Register_Virtual_Stack_Slices
>
>and
>
>Transform Virtual Stack Slices
>
>http://pacific.mpi-
cbg.de/wiki/index.php/Transform_Virtual_Stack_Slices
>
>they incorporate bUnwarpJ, feature based registration and
allow you to
>save the estimated transformation and apply it to other
images later.
>
>Good luck,
>Stephan
>
>
>On Wed, 2010-12-15 at 11:24 +1100, James Burchfield wrote:
>> I am looking for a simple way to measure the transformation
>> required to achieve proper image registration between a set
of
>> reference images and then to apply this same transformation
to a
>> stack.
>> I have been able to achieve fantastic results with bUnwarpJ
on
>> the reference image, but cannot work out how to apply this
to
>> other images.
>> MultiStackReg works well on some data sets, but ideally i
would
>> like to apply exactly the same transformation to every
image.
>> Cheers,
>> James

[Stephan Saalfeld]

Hi James,

you can do that in two ways.

1. Create the one transformation file by registering the two reference
images.  Then make symlinks to that transformation file for each image
you want to transform.  Use Transform Virtual Stack Slices to transform
all the images using the symlinked files.

2. Create a script that does it.  If I find some minutes I can help with
that later.

Best,
Stephan

On Thu, 2010-12-16 at 10:25 +1100, James Burchfield wrote:

> Thanks Stephan,
> I have already played with these plugins but cannot get them
> to do what i want.  The Transform Virtual Stack Slices plugin
> appears to require a separate transformation file for every
> image,  what i want to do is apply a single transformation to
> multiple images.  Is this possible with those plugins?
> James
>
> >
> >Check the Fiji plugins
> >
> >Register Virtual Stack Slices
> >
> >http://pacific.mpi-
> cbg.de/wiki/index.php/Register_Virtual_Stack_Slices
> >
> >and
> >
> >Transform Virtual Stack Slices
> >
> >http://pacific.mpi-
> cbg.de/wiki/index.php/Transform_Virtual_Stack_Slices
> >
> >they incorporate bUnwarpJ, feature based registration and
> allow you to
> >save the estimated transformation and apply it to other
> images later.
> >
> >Good luck,
> >Stephan
> >
> >
> >On Wed, 2010-12-15 at 11:24 +1100, James Burchfield wrote:
> >> I am looking for a simple way to measure the transformation
> >> required to achieve proper image registration between a set
> of
> >> reference images and then to apply this same transformation
> to a
> >> stack.
> >> I have been able to achieve fantastic results with bUnwarpJ
> on
> >> the reference image, but cannot work out how to apply this
> to
> >> other images.
> >> MultiStackReg works well on some data sets, but ideally i
> would
> >> like to apply exactly the same transformation to every
> image.
> >> Cheers,
> >> James