Discussion:
Image Registration
James Burchfield
2010-12-15 00:24:30 UTC
Permalink
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
2010-12-15 09:37:40 UTC
Permalink
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
Post by James Burchfield
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
James Burchfield
2010-12-15 23:25:23 UTC
Permalink
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
Post by Stephan Saalfeld
Check the Fiji plugins
Register Virtual Stack Slices
http://pacific.mpi-
cbg.de/wiki/index.php/Register_Virtual_Stack_Slices
Post by Stephan Saalfeld
and
Transform Virtual Stack Slices
http://pacific.mpi-
cbg.de/wiki/index.php/Transform_Virtual_Stack_Slices
Post by Stephan Saalfeld
they incorporate bUnwarpJ, feature based registration and
allow you to
Post by Stephan Saalfeld
save the estimated transformation and apply it to other
images later.
Post by Stephan Saalfeld
Good luck,
Stephan
Post by James Burchfield
I am looking for a simple way to measure the transformation
required to achieve proper image registration between a set
of
Post by Stephan Saalfeld
Post by James Burchfield
reference images and then to apply this same transformation
to a
Post by Stephan Saalfeld
Post by James Burchfield
stack.
I have been able to achieve fantastic results with bUnwarpJ
on
Post by Stephan Saalfeld
Post by James Burchfield
the reference image, but cannot work out how to apply this
to
Post by Stephan Saalfeld
Post by James Burchfield
other images.
MultiStackReg works well on some data sets, but ideally i
would
Post by Stephan Saalfeld
Post by James Burchfield
like to apply exactly the same transformation to every
image.
Post by Stephan Saalfeld
Post by James Burchfield
Cheers,
James
Stephan Saalfeld
2010-12-16 09:32:13 UTC
Permalink
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
Post by James Burchfield
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
Post by Stephan Saalfeld
Check the Fiji plugins
Register Virtual Stack Slices
http://pacific.mpi-
cbg.de/wiki/index.php/Register_Virtual_Stack_Slices
Post by Stephan Saalfeld
and
Transform Virtual Stack Slices
http://pacific.mpi-
cbg.de/wiki/index.php/Transform_Virtual_Stack_Slices
Post by Stephan Saalfeld
they incorporate bUnwarpJ, feature based registration and
allow you to
Post by Stephan Saalfeld
save the estimated transformation and apply it to other
images later.
Post by Stephan Saalfeld
Good luck,
Stephan
Post by James Burchfield
I am looking for a simple way to measure the transformation
required to achieve proper image registration between a set
of
Post by Stephan Saalfeld
Post by James Burchfield
reference images and then to apply this same transformation
to a
Post by Stephan Saalfeld
Post by James Burchfield
stack.
I have been able to achieve fantastic results with bUnwarpJ
on
Post by Stephan Saalfeld
Post by James Burchfield
the reference image, but cannot work out how to apply this
to
Post by Stephan Saalfeld
Post by James Burchfield
other images.
MultiStackReg works well on some data sets, but ideally i
would
Post by Stephan Saalfeld
Post by James Burchfield
like to apply exactly the same transformation to every
image.
Post by Stephan Saalfeld
Post by James Burchfield
Cheers,
James
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