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StackReg or similar

Rainer M. Engel
Hello everyone,

I have a filtered stack which works very nice with StackReg, but in
addition to a well aligned stack I would like to get the used
transformations (in modes transform and rigid i.e.).
My focus lies only on the position offsets.

Something like verbose to log would be fine.

If not possible, is there another way to get these values?

Thanks for time.

Regards,
Rainer


--
Rainer M. Engel, Dipl. Digital Artist
scientific|Media GbR
Pichelsdorferstr. 143
D-13595 Berlin

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Re: StackReg or similar

Jacob Keller
Try the image stabilizer plugin--log tells you number of pixels moved in x
and y, and you can also specify the amount that the initial template
changes, using the template update coefficient.

Jacob

On Thu, Sep 27, 2012 at 11:44 AM, Rainer M. Engel <[hidden email]> wrote:

> Hello everyone,
>
> I have a filtered stack which works very nice with StackReg, but in
> addition to a well aligned stack I would like to get the used
> transformations (in modes transform and rigid i.e.).
> My focus lies only on the position offsets.
>
> Something like verbose to log would be fine.
>
> If not possible, is there another way to get these values?
>
> Thanks for time.
>
> Regards,
> Rainer
>
>
> --
> Rainer M. Engel, Dipl. Digital Artist
> scientific|Media GbR
> Pichelsdorferstr. 143
> D-13595 Berlin
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>



--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [hidden email]
*******************************************

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Re: StackReg or similar

Unruh, Jay-2
In reply to this post by Rainer M. Engel
Rainer,

I wrote my own version of StackReg (needs TurboReg installed) that will output a translational trajectory along with the registration.  You can download it from my website (http://research.stowers.org/imagejplugins/) and it will show up in Plugins>Image Tools>StackRegJ.

Jay

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Rainer M. Engel
Sent: Thursday, September 27, 2012 11:45 AM
To: [hidden email]
Subject: StackReg or similar

Hello everyone,

I have a filtered stack which works very nice with StackReg, but in addition to a well aligned stack I would like to get the used transformations (in modes transform and rigid i.e.).
My focus lies only on the position offsets.

Something like verbose to log would be fine.

If not possible, is there another way to get these values?

Thanks for time.

Regards,
Rainer


--
Rainer M. Engel, Dipl. Digital Artist
scientific|Media GbR
Pichelsdorferstr. 143
D-13595 Berlin

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
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Re: StackReg or similar

Rainer M. Engel
Thank you both for your tips. Both appear very promising.

Very cool.

Ahoi,
Rainer


Am 27.09.2012 19:08, schrieb Unruh, Jay:

> Rainer,
>
> I wrote my own version of StackReg (needs TurboReg installed) that will output a translational trajectory along with the registration.  You can download it from my website (http://research.stowers.org/imagejplugins/) and it will show up in Plugins>Image Tools>StackRegJ.
>
> Jay
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Rainer M. Engel
> Sent: Thursday, September 27, 2012 11:45 AM
> To: [hidden email]
> Subject: StackReg or similar
>
> Hello everyone,
>
> I have a filtered stack which works very nice with StackReg, but in addition to a well aligned stack I would like to get the used transformations (in modes transform and rigid i.e.).
> My focus lies only on the position offsets.
>
> Something like verbose to log would be fine.
>
> If not possible, is there another way to get these values?
>
> Thanks for time.
>
> Regards,
> Rainer
>
>
> --
> Rainer M. Engel, Dipl. Digital Artist
> scientific|Media GbR
> Pichelsdorferstr. 143
> D-13595 Berlin
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>


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Re: StackReg or similar

Kenton Arkill
In reply to this post by Rainer M. Engel
'Register Virtual Stack Slices' does what you want (if I understand you correctly).
Kenton

Kenton Arkill
GB U23 Ladies'
Underwater Hockey Coach
GB Masters
Underwater Hockey Manager




On 27 Sep 2012, at 17:44, Rainer M. Engel wrote:

> Hello everyone,
>
> I have a filtered stack which works very nice with StackReg, but in
> addition to a well aligned stack I would like to get the used
> transformations (in modes transform and rigid i.e.).
> My focus lies only on the position offsets.
>
> Something like verbose to log would be fine.
>
> If not possible, is there another way to get these values?
>
> Thanks for time.
>
> Regards,
> Rainer
>
>
> --
> Rainer M. Engel, Dipl. Digital Artist
> scientific|Media GbR
> Pichelsdorferstr. 143
> D-13595 Berlin
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html


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Re: StackReg or similar

Christian Tischer
Hello,

regarding this dicussions:

do the StackReg and  Image stabilizer have a parameter to tell it how large
the maximal pixel shift between images can be?

we have some data, where it seems to fail the registration if the shift is
too large.

Tischi


On Fri, Sep 28, 2012 at 9:39 AM, Kenton Arkill <[hidden email]>wrote:

> 'Register Virtual Stack Slices' does what you want (if I understand you
> correctly).
> Kenton
>
> Kenton Arkill
> GB U23 Ladies'
> Underwater Hockey Coach
> GB Masters
> Underwater Hockey Manager
>
>
>
>
> On 27 Sep 2012, at 17:44, Rainer M. Engel wrote:
>
> > Hello everyone,
> >
> > I have a filtered stack which works very nice with StackReg, but in
> > addition to a well aligned stack I would like to get the used
> > transformations (in modes transform and rigid i.e.).
> > My focus lies only on the position offsets.
> >
> > Something like verbose to log would be fine.
> >
> > If not possible, is there another way to get these values?
> >
> > Thanks for time.
> >
> > Regards,
> > Rainer
> >
> >
> > --
> > Rainer M. Engel, Dipl. Digital Artist
> > scientific|Media GbR
> > Pichelsdorferstr. 143
> > D-13595 Berlin
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: StackReg or similar

Rainer M. Engel
In reply to this post by Rainer M. Engel
Am 27.09.2012 18:44, schrieb Rainer M. Engel:

> Hello everyone,
>
> I have a filtered stack which works very nice with StackReg, but in
> addition to a well aligned stack I would like to get the used
> transformations (in modes transform and rigid i.e.).
> My focus lies only on the position offsets.
>
> Something like verbose to log would be fine.
>
> If not possible, is there another way to get these values?
>
> Thanks for time.
>
> Regards,
> Rainer
>
>


I made some tests. If anybody is interested.

ZIP-ARCHIVE:
https://dl.dropbox.com/u/414433/imagej/aligning.zip

It Contains:
- s03_SOURCE.tif
- s03_StackReg.tif (very fast and good)

(not good/fast enough (maybe there are to me unknown tweaks))
- s03_ImageStabilizer.tif
- s03_RegVirtualStacks_Rigid.tif
- s03_RegVirtualStacks_Transformation.tif


I think there are purposes, when the actual registration with its
sampling is not needed and could be disabled to only get transformation
data for speed reasons.

Regards,
Rainer


--
Rainer M. Engel, Dipl. Digital Artist
scientific|Media GbR
Pichelsdorferstr. 143
D-13595 Berlin

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Re: StackReg or similar

Jacob Keller
On Fri, Sep 28, 2012 at 9:34 AM, Jacob Keller <
[hidden email]> wrote:

> It Contains:
>> - s03_SOURCE.tif
>> - s03_StackReg.tif (very fast and good)
>>
>> (not good/fast enough (maybe there are to me unknown tweaks))
>> - s03_ImageStabilizer.tif
>> - s03_RegVirtualStacks_Rigid.tif
>> - s03_RegVirtualStacks_Transformation.tif
>>
>>
>> I think there are purposes, when the actual registration with its
>> sampling is not needed and could be disabled to only get transformation
>> data for speed reasons.
>>
>> Regards,
>> Rainer
>>
>
> I liked playing a bit with the data set with a macro I wrote: my thinking
> was to make a macro which first makes a stack average (z-project), then
> aligns the whole stack to that, iterates until some convergence level is
> met. I think, though, that this process can get stuck in a local minimum,
> say if there are two roughly equivalent registrations, and I am not sure
> how to avoid that. One thing I think that is missing from stackreg is the
> ability to align all images to one reference image, so that the stack does
> not drift over time. So actually, I just tried stackreg first, then my
> iterative macro, and it works great! I won't attach it, as it is ~3MB, but
> it has both no drift and excellent image-to-image registration. I'll send
> it individually if you want.
>
> JPK
>
>
>
>
> *******************************************
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> email: [hidden email]
> *******************************************
>



--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [hidden email]
*******************************************

--
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