Registering two stacks and before merging

[lechristophe]

Hi,

I would like to merge two stacks (red and green) but one of them has a
constant drift, that is one is shifted off a few pixels compared to the
other. Do you know any function/macro/plugin that allos to interactively
superpose the two stacks (based on the two first images) to get the offset
visually, then actually merge the two stacks ? For the moment I use canvas
extension and cropping but I have to do a trial/error procedure, pixel by
pixel to estimate the offset...

Thank you for your ideas,

Christophe Leterrier

Postdoc
INSERM UMR641 Neurobiology of ionic channels
IFR Jean Roche - Mediterranee University
Marseille, France

[Joel Sheffield]

What about converting each to RGB, (with the correct colors), and
then using Copy>Paste with the paste filter set a blend?  It seems to
me that you can move one image over the other until you are
satisfied.  You may still have to extend the canvas on one of the
stacks, though.

You might also be able to add one image from stack 1 to stack 2, and
then use the Stack-Reg plugin to align the stack.

Joel


Date sent:       Fri, 11 Jan 2008 17:26:37 +0100
Send reply to:   ImageJ Interest Group <[hidden email]>
From:           Christophe Leterrier
<[hidden email]>
Subject:         Registering two stacks and before merging
To:             [hidden email]

> Hi,
>
> I would like to merge two stacks (red and green) but one of them has a
> constant drift, that is one is shifted off a few pixels compared to the
> other. Do you know any function/macro/plugin that allos to interactively
> superpose the two stacks (based on the two first images) to get the offset
> visually, then actually merge the two stacks ? For the moment I use canvas
> extension and cropping but I have to do a trial/error procedure, pixel by
> pixel to estimate the offset...
>
> Thank you for your ideas,
>
> Christophe Leterrier
>
> Postdoc
> INSERM UMR641 Neurobiology of ionic channels
> IFR Jean Roche - Mediterranee University
> Marseille, France

--
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

[Tony Collins-4]

I think Gabriel's "Align RGB planes" plugin
(http://www.dentistry.bham.ac.uk/landinig/software/software.html) nearly
does what you want, in that you can align the channels after merging.
I'm not sure if it will align all slices at once or one at a time
though.
Maybe a small tweak?
Best,
Tony


Tony J. Collins, Ph.D.
McMaster Biophotonics Facility
Dept. Biochemistry and Biomedical Sciences HSC 4H21A
McMaster University, Hamilton, ON, L8N 3Z5
[phone] x28812(off.)/x26488(lab)
[hidden email]     www.macbiophotonics.ca

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Christophe Leterrier
> Sent: January 11, 2008 11:27 AM
> To: [hidden email]
> Subject: Registering two stacks and before merging
>
> Hi,
>
> I would like to merge two stacks (red and green) but one of them has a
> constant drift, that is one is shifted off a few pixels compared to

the
> other. Do you know any function/macro/plugin that allos to
interactively
> superpose the two stacks (based on the two first images) to get the
offset
> visually, then actually merge the two stacks ? For the moment I use
canvas
> extension and cropping but I have to do a trial/error procedure, pixel
by

> pixel to estimate the offset...
>
> Thank you for your ideas,
>
> Christophe Leterrier
>
> Postdoc
> INSERM UMR641 Neurobiology of ionic channels
> IFR Jean Roche - Mediterranee University
> Marseille, France

[Knecht, David]

I am pretty sure it only does one at a time.  It would be really nice  
if it were updated to do the entire stack.  Dave

On Jan 11, 2008, at 1:27 PM, Tony Collins wrote:

> I think Gabriel's "Align RGB planes" plugin
> (http://www.dentistry.bham.ac.uk/landinig/software/software.html)  
> nearly
> does what you want, in that you can align the channels after merging.
> I'm not sure if it will align all slices at once or one at a time
> though.
> Maybe a small tweak?
> Best,
> Tony
>
>
> Tony J. Collins, Ph.D.
> McMaster Biophotonics Facility
> Dept. Biochemistry and Biomedical Sciences HSC 4H21A
> McMaster University, Hamilton, ON, L8N 3Z5
> [phone] x28812(off.)/x26488(lab)
> [hidden email]     www.macbiophotonics.ca
>
>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>> Christophe Leterrier
>> Sent: January 11, 2008 11:27 AM
>> To: [hidden email]
>> Subject: Registering two stacks and before merging
>>
>> Hi,
>>
>> I would like to merge two stacks (red and green) but one of them  
>> has a
>> constant drift, that is one is shifted off a few pixels compared to
> the
>> other. Do you know any function/macro/plugin that allos to
> interactively
>> superpose the two stacks (based on the two first images) to get the
> offset
>> visually, then actually merge the two stacks ? For the moment I use
> canvas
>> extension and cropping but I have to do a trial/error procedure,  
>> pixel
> by
>> pixel to estimate the offset...
>>
>> Thank you for your ideas,
>>
>> Christophe Leterrier
>>
>> Postdoc
>> INSERM UMR641 Neurobiology of ionic channels
>> IFR Jean Roche - Mediterranee University
>> Marseille, France

Dr. David Knecht
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)

[Gabriel Landini]

On Friday 11 January 2008, David Knecht wrote:
> I am pretty sure it only does one at a time.  It would be really nice
> if it were updated to do the entire stack.

Yes, it does one at a time. I just modified it so it can do all slices in the
stack, but I have little time to do any thorough testing. If anybody wants to
try it at this stage and report back any bugs, please mail me directly and I
will send a copy.

Regards,

Gabriel