Image Stabilizer / StackReg plugins feature request

[lechristophe]

Dear all,

I'm using Kang Li's Images Stabilizer or the EPFL StackReg to eliminate xy
drift in time lapse series. However, I have several wavelength and I would
like to register the first wavelength (reference wavelength, then use the
exact shifts that have been applied to this sequence to process the other
wavelength (to keep wavelength images "aligned"). Would it be possible to
modify one of these two plugins in order to be able to save/log the
calculated shifts, and then load/reapply them on another stack ? Would
anyone but me find that feature usefull ?

Thanks,

Christophe Leterrier

[Colin Poczatek]

I did something similar for our pluggin, registering 4 coupled stacks
by registering one.  All I did was make a copy of the one stack (I
didn't want to dig too deep into the StackReg/TurboReg code out of
sloth) and pass that to a modified version of StackReg which returneds
an array of translations which get applied to each plane (we also only
wanted translations).  There's a variable in the StackReg code that's a
matrix for the transformation, and if you just want a translation it's
easy to grab a copy of those values at each step.

I can send you the code if you want...

Collin


Quoting Christophe Leterrier <[hidden email]>:

> Dear all,
>
> I'm using Kang Li's Images Stabilizer or the EPFL StackReg to eliminate xy
> drift in time lapse series. However, I have several wavelength and I would
> like to register the first wavelength (reference wavelength, then use the
> exact shifts that have been applied to this sequence to process the other
> wavelength (to keep wavelength images "aligned"). Would it be possible to
> modify one of these two plugins in order to be able to save/log the
> calculated shifts, and then load/reapply them on another stack ? Would
> anyone but me find that feature usefull ?
>
> Thanks,
>
> Christophe Leterrier
>

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[Daniel Woods]

I'm interested in this too - I have a 3D stack of speckle images (OCT) which align much better if I apply a filter first (Median either Sigma Filter Plus), but I want to preserve the unfiltered speckle information for later processing using a 3D filter macro.

Colin do you still have the modified Stackreg code?  Does anyone else have any ideas?

Dan

[Colin Poczatek]

Apparently emails with attached .java files bounce...
Let me know if you want the file...

>> Colin do you still have the modified Stackreg code?  Does anyone else have
>> any ideas?
>>  
You're not the guy that emailed me a few weeks ago?  I must be getting
popular.  :)
If you want to use TurboReg and not something else short answer: use
this plugin

http://www.stanford.edu/~bbusse/work/downloads.html


Changing the code I've attached might be a little bit of a pain...

This is what I said to him:
------------------------------------------------------

Sorry I didn't get back to you sooner. I've attached a copy of the
modified StackReg.java, however our code is pretty complicated since
we're trying to do multithreaded things and keep track of state and
such. But if you look at the return values of the track() method in what
I've attached gives you then need to do something like:

double[][] translations = AutoTrack.track(imagePlus);
deltax = (-1.0) * translations[i][0];
deltay = (-1.0) * translations[i][1];

loop over all images[] in an array

images[k].killRoi();
images[k].setSlice(plane);
images[k].getProcessor().translate(0.0, deltay);
images[k].getProcessor().translate(deltax, 0.0);

end loop


But that being said it would probably be easier to use the MultiStackReg
plugin some one pointed out to me last week. It can save any
transformation StackReg generates in a file which can then be applied to
other images.
http://www.stanford.edu/~bbusse/work/downloads.html

Collin




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[Daniel Woods]

You are getting popular, I only registered today!  Many thanks Colin, huge thanks for the swift reply.  I tried it already and it works like a geeky dream.