http://imagej.273.s1.nabble.com/registering-a-stack-advice-needed-tp5020546p5020569.html
> On 24 Apr 2018, at 21:36 , Saalfeld, Stephan <
[hidden email]> wrote:
>
> 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 : +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.
>>>
>>> --
>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>
>>> --
>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
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