Image registration correction

[simon walker (BI)]

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Hello,
Not a confocal question, but I know you are a knowledgeable crowd.  We are
in the process of setting up a screen looking at the colocalisation between
two subcellular compartments which appear as small red and green spots.  
Initial tests have revealed an image registration problem where the same
fluorescent beads are not correctly overlaid in the red and green channels.  
Curiously the registration off-set is not consitent across the image, so a
straightforward pixel-shift correction will not work.  Can anyone suggest a
good (preferarbly ImageJ based) method to create and subsequently apply a
shift-correction map so that the green and red channels correctly align?  I've
had a quick look at the registration options in FIJI and there seem to be
multiple options which might do the trick, but I don't know how any of them
work and which is the best solution.  Advice please!
Thanks,
Simon

P.S. I realise that an alternative solution would be to identify and correct the
source of the registration problem, but I've looked at the most likely causes
and not been able to do this.

[Stanislav Vitha-2]

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I have had a similar problem on our confocal system.
The UnwarpJ plugin for ImageJ  (http://bigwww.epfl.ch/thevenaz/UnwarpJ/)
allows you to load two images of your multicolor beads, run the affine
transform procedure to warp one of the images to get a match.

In the Advanced Options, if you click on "Save transformation" the computed
deformation is saved at the end of the process. All the B-spline coefficients,
and relevant information to recover this deformation is saved in a file specified
by the user through a File Dialog. Use "Load transformation" in the I/O menu of
the Toolbar to read this transformation and apply it to the image of a real
sample.

Stan Vitha
Microscopy and Imaging Center
Texas A&M University

On Wed, 27 Mar 2013 06:41:49 -0500, Simon Walker
<[hidden email]> wrote:

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>http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
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>
>Hello,
>Not a confocal question, but I know you are a knowledgeable crowd.  We are
>in the process of setting up a screen looking at the colocalisation between
>two subcellular compartments which appear as small red and green spots.  
>Initial tests have revealed an image registration problem where the same
>fluorescent beads are not correctly overlaid in the red and green channels.  
>Curiously the registration off-set is not consitent across the image, so a
>straightforward pixel-shift correction will not work.  Can anyone suggest a
>good (preferarbly ImageJ based) method to create and subsequently apply a
>shift-correction map so that the green and red channels correctly align?  I've
>had a quick look at the registration options in FIJI and there seem to be
>multiple options which might do the trick, but I don't know how any of them
>work and which is the best solution.  Advice please!
>Thanks,
>Simon
>
>P.S. I realise that an alternative solution would be to identify and correct the
>source of the registration problem, but I've looked at the most likely causes
>and not been able to do this.

[simon walker (BI)-2]

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Hi Stan,
Thanks very much for this suggestion.  I've finally had time to try it and the Unwarp plugin seems to work very nicely.
Best wishes,
Simon


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Stanislav Vitha
Sent: 28 March 2013 18:51
To: [hidden email]
Subject: Re: Image registration correction

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I have had a similar problem on our confocal system.
The UnwarpJ plugin for ImageJ  (http://bigwww.epfl.ch/thevenaz/UnwarpJ/)
allows you to load two images of your multicolor beads, run the affine transform procedure to warp one of the images to get a match.

In the Advanced Options, if you click on "Save transformation" the computed deformation is saved at the end of the process. All the B-spline coefficients, and relevant information to recover this deformation is saved in a file specified by the user through a File Dialog. Use "Load transformation" in the I/O menu of the Toolbar to read this transformation and apply it to the image of a real sample.

Stan Vitha
Microscopy and Imaging Center
Texas A&M University

On Wed, 27 Mar 2013 06:41:49 -0500, Simon Walker <[hidden email]> wrote:

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>To join, leave or search the confocal microscopy listserv, go to:
>http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>*****
>
>Hello,
>Not a confocal question, but I know you are a knowledgeable crowd.  We
>are in the process of setting up a screen looking at the colocalisation
>between two subcellular compartments which appear as small red and green spots.
>Initial tests have revealed an image registration problem where the
>same fluorescent beads are not correctly overlaid in the red and green channels.
>Curiously the registration off-set is not consitent across the image,
>so a straightforward pixel-shift correction will not work.  Can anyone
>suggest a good (preferarbly ImageJ based) method to create and
>subsequently apply a shift-correction map so that the green and red
>channels correctly align?  I've had a quick look at the registration
>options in FIJI and there seem to be multiple options which might do
>the trick, but I don't know how any of them work and which is the best solution.  Advice please!
>Thanks,
>Simon
>
>P.S. I realise that an alternative solution would be to identify and
>correct the source of the registration problem, but I've looked at the
>most likely causes and not been able to do this.

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[Johannes Schindelin]

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Hi Simon,

On Tue, 11 Jun 2013, simon walker wrote:

> Thanks very much for this suggestion.  I've finally had time to try it
> and the Unwarp plugin seems to work very nicely.

Please note that UnwarpJ is superseded by bUnwarpJ:
http://fiji.sc/BUnwarpJ

Ciao,
Johannes

[JOEL B. SHEFFIELD]

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Hi,

I just checked the bUnwarpJ site listed below, and the link, to the Jenkins
archive, seems to list only UnwarpJ, and not bUnwarpj. What am I doing
wrong?

Joel


On Tue, Jun 11, 2013 at 11:24 AM, Johannes Schindelin
<[hidden email]>wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi Simon,
>
> On Tue, 11 Jun 2013, simon walker wrote:
>
> > Thanks very much for this suggestion.  I've finally had time to try it
> > and the Unwarp plugin seems to work very nicely.
>
> Please note that UnwarpJ is superseded by bUnwarpJ:
> http://fiji.sc/BUnwarpJ
>
> Ciao,
> Johannes
>

--


Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs

[Johannes Schindelin]

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Hi,

On Tue, 11 Jun 2013, JOEL B. SHEFFIELD wrote:

> On Tue, Jun 11, 2013 at 11:24 AM, Johannes Schindelin
> <[hidden email]>wrote:
>
> > On Tue, 11 Jun 2013, simon walker wrote:
> >
> > > Thanks very much for this suggestion.  I've finally had time to try it
> > > and the Unwarp plugin seems to work very nicely.
> >
> > Please note that UnwarpJ is superseded by bUnwarpJ:
> > http://fiji.sc/BUnwarpJ
>
> I just checked the bUnwarpJ site listed below, and the link, to the Jenkins
> archive, seems to list only UnwarpJ, and not bUnwarpj. What am I doing
> wrong?

Ignacio Arganda-Carreras (the author of bUnwarpJ and former student of the
author of UnwarpJ) fixed the link sometime in the past two hours. Do you
still get the wrong file?

Ciao,
Johannes