registering stack in the presence of radial expansion (scale)

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registering stack in the presence of radial expansion (scale)

Kenneth R Sloan-2
I’m not very conversant in the details of registering a stack of images, but I’m involved in a couple of projects that are doing this successfully in ImageJ.  There is another project which is having difficulty.

The problem seems to be that some images in the stack are at a slightly different SCALE.  The people looking at the images describe it as “radial expansion”.

So…I’m looking for expert advice:

a) does ImageJ have a stack registration plugin that can deal with scaling?
b) if so…can you please get me started on using it?

--
Kenneth Sloan
[hidden email] <mailto:[hidden email]>
Vision is the art of seeing what is invisible to others.





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Re: registering stack in the presence of radial expansion (scale)

Christian Goosmann-2
Dear Kenneth
I would suggest trying TrakEM2. It is a bit of a learning curve but
there is good documentation  around. You could import your stack into a
set of different layers and align them using automatic functions within
the plugin. In this automatic alignment there is a way of setting a
layer as template (to be left untransformed) and to set the possible
transformations for the other layers (from rigid to affine). That can
take care of all kind of scaling and distortion between slices. There is
the possibility of using manual alignment with landmarks in case there
are too few features the algorithm can detect automatically. In the end
you can export back into a tiff stack.
Hth
Christian

---
Christian Goosmann
Mikroskopie
Max-Planck-Institut für Infektionsbiologie
Campus Charité Mitte
Charitéplatz 1
10117 Berlin
Tel.: +49 30 28460 388

Kenneth Sloan wrote:

> I’m not very conversant in the details of registering a stack of images, but I’m involved in a couple of projects that are doing this successfully in ImageJ.  There is another project which is having difficulty.
>
> The problem seems to be that some images in the stack are at a slightly different SCALE.  The people looking at the images describe it as “radial expansion”.
>
> So…I’m looking for expert advice:
>
> a) does ImageJ have a stack registration plugin that can deal with scaling?
> b) if so…can you please get me started on using it?
>
> --
> Kenneth Sloan
> [hidden email] <mailto:[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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Re: registering stack in the presence of radial expansion (scale)

Kenneth R Sloan-2
Thanks - we’ll try it.

--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.




> On Oct 26, 2015, at 05:32 , Christian Goosmann <[hidden email]> wrote:
>
> Dear Kenneth
> I would suggest trying TrakEM2. It is a bit of a learning curve but there is good documentation  around. You could import your stack into a set of different layers and align them using automatic functions within the plugin. In this automatic alignment there is a way of setting a layer as template (to be left untransformed) and to set the possible transformations for the other layers (from rigid to affine). That can take care of all kind of scaling and distortion between slices. There is the possibility of using manual alignment with landmarks in case there are too few features the algorithm can detect automatically. In the end you can export back into a tiff stack.
> Hth
> Christian
>
> ---
> Christian Goosmann
> Mikroskopie
> Max-Planck-Institut für Infektionsbiologie
> Campus Charité Mitte
> Charitéplatz 1
> 10117 Berlin
> Tel.: +49 30 28460 388
>
> Kenneth Sloan wrote:
>> I’m not very conversant in the details of registering a stack of images, but I’m involved in a couple of projects that are doing this successfully in ImageJ.  There is another project which is having difficulty.
>>
>> The problem seems to be that some images in the stack are at a slightly different SCALE.  The people looking at the images describe it as “radial expansion”.
>>
>> So…I’m looking for expert advice:
>>
>> a) does ImageJ have a stack registration plugin that can deal with scaling?
>> b) if so…can you please get me started on using it?
>>
>> --
>> Kenneth Sloan
>> [hidden email] <mailto:[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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ImageJ mailing list: http://imagej.nih.gov/ij/list.html