http://imagej.273.s1.nabble.com/registering-a-stack-advice-needed-tp5020546p5020555.html
I'm willing to try other methods. My constraints are:
order - there is no systematic drift. Just a bunch of images of the
> 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-plugin> 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 : +33(0)3 68 85 41 84
>
> -----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.
>
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