Re: registering a stack - advice needed

Posted by Saalfeld, Stephan on Apr 25, 2018; 2:36am
URL: http://imagej.273.s1.nabble.com/registering-a-stack-advice-needed-tp5020546p5020568.html

Hi Ken,

Please try

https://github.com/axtimwalde/mpicbg/blob/master/mpicbg/src/main/java/m
picbg/models/InterpolatedAffineModel2D.java

as the filterRansac model with 0.1 affine and 0.9 translation (or
something along those lines).
 
Then use the inliers to do an affine.

Some scripting required but there are many examples floating around in
this mailing list or elsewhere in the Internet (may be here

https://github.com/axtimwalde/fiji-scripts

).

Best,
Stephan


On Mon, 2018-04-23 at 09:20 -0500, Kenneth Sloan wrote:

> Thanks for your comments.
>
> I've been using SIFT in a number of projects.
>
> Limiting it to "translation only" eliminates the disasters,
> but I really need a SMALL amount of scaling and rotation.
>
> The core question is: how can I get a small amount
> of scaling and rotation, without giving SIFT license
> to rotate by 90deg?
>
> I'm willing to try other methods.  My constraints are:
>  *ImageJ implementation
>  *translation, scale, rotation, perhaps elastic deformation - but all
> LIMITED
>  *automatic (no user interaction)
>
> To be clear, the images in the current stacks are not in any
> particular
> order - there is no systematic drift.  Just a bunch of images of the
> same scene, taken at different times using different imaging
> modalities.
>
> The gray-level differences are major - but the primary source of
> useful
> registration features are uniformly DARK compared with the
> surrounding
> area.
>
> In a way, this is not unlike ancient stereo-pair matching problems
> from the
> 1970's - the two images may vary in perspective, but matching
> features
> should lie in a small horizontal band.
>
> Hmmm...I'm drifting perilously close to feeling the urge to roll my
> own.
> I don't really want to do that, but I suppose it's an option.
>
> SIFT does so many other things very well; I'm loathe to abandon it.
>
>
> --
> Kenneth Sloan
> [hidden email]
> Vision is the art of seeing what is invisible to others.
>
>
>
>
>
> > On 23 Apr 2018, at 03:21 , Philippe CARL <[hidden email]>
> > wrote:
> >
> > Dear Kenneth,
> > I had/have similar applications for which I took quite some time
> > before
> > finding a stable and reproducible solution.
> > So first I started with the TurboReg and StackReg solutions:
> > http://bigwww.epfl.ch/thevenaz/turboreg/
> > http://bigwww.epfl.ch/thevenaz/stackreg/
> > to later on move over the JavaSIFT:
> > http://fly.mpi-cbg.de/~saalfeld/Projects/javasift.html
> > https://imagej.net/Feature_Extraction
> > which more often gave me better results but there were cases
> > (similarly to
> > what you reported) where for whatever reason the algorithm was
> > giving crazy
> > results.
> > And now I use the Slice Alignment plugin:
> > https://sites.google.com/site/qingzongtseng/template-matching-ij-pl
> > ugin
> > which in my case (I have nevertheless to precise that I have only
> > translation transformations, i.e. no scaling and rotation) is
> > giving me good
> > results.
> > And given that this Slice Alignment plugin is only applying
> > translation
> > transformations, I would recommend you to try to first apply it on
> > your
> > pictures followed then by the SIFT algorithm in order to take care
> > the
> > rotation and scaling transformations.
> > Good luck!!!
> > My best regards,
> > Philippe
> >
> > Philippe CARL
> > Laboratoire de Bioimagerie et Pathologies
> > UMR 7021 CNRS - Université de Strasbourg
> > Faculté de Pharmacie
> > 74 route du Rhin
> > 67401 ILLKIRCH
> > Tel : [phone]
> >
> > -----Message d'origine-----
> > De : ImageJ Interest Group [mailto:[hidden email]] De la part
> > de
> > Kenneth Sloan
> > Envoyé : lundi 23 avril 2018 03:38
> > À : [hidden email]
> > Objet : registering a stack - advice needed
> >
> > I have an application which needs to do MINOR corrections to images
> > in
> > a Stack in order to register them.  The modifications involve
> > TRANSLATION,
> > some ROTATION, and SCALING (perhaps anisotropic).
> >
> > So far, SIFT has been what I've been using.  
> >
> > My problem is that all of the above transformations are small - but
> > I
> > don't know how to limit the allowed ROTATION (in
> > particular).  ROTATION
> > is the problem child, because the one way that SIFT produces
> > ridiculous
> > results is to rotate a given image by 90deg - presumably because it
> > finds
> > some accidental arrangement of features that makes it look like
> > this is a
> > good
> > idea.
> >
> > SIFT allows you to specify a limit on the number of pixels to MOVE
> > - but
> > this does not
> > seem to constrain the ROTATION.
> >
> > So...bottom line: I'm looking for advice on other methods to try.  
> >
> > The key requirement is that I'd like to allow TRANSLATION,
> > anisotropic
> > SCALE,
> > and ROTATION - even arbitrary local warping.  BUT, I would also
> > like to put
> > strict limits on "how much" of each is allowed.
> >
> > As a rough guideline - I'd say  that I need to limit:
> >
> >   TRANSLATION - no more than 25 pixels (in a 750x750 image)
> >   SCALE - in the range [.9, 1.1] in x and y (independent)
> >   ROTATION - no more than 10deg
> >
> > Now...I naively thought that specifying "25 pixels max" would do
> > the trick,
> > but I occasionally see results where the image is rotated 90deg,
> > and
> > "matching features"
> > are hundreds of pixels apart.  Is this expected?  or is it a bug?
> >
> >
> > I can supply an example pair of images that exhibits this behavior
> > - on
> > request.
> >
> >
> > My current workaround is to specify "translation only" with a
> > maximum of 25
> > pixels of motion,
> > and am living with the slight inaccuracies due to the lack of
> > scaling &
> > rotation.  As noted
> > above, the (spatial) differences between images in the stack are
> > small, so
> > this is
> > not a tragedy.  [the gray-scale differences can be huge - this is
> > "multi-modal imaging".
> >
> > --
> > Kenneth Sloan
> > [hidden email]
> > Vision is the art of seeing what is invisible to others.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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