help with TrakEM2 alignment

[inesica]

Hello everybody!
I had a question about manual realignment with TrakEM2. I can align in x-y and also rotate, however I was wondering if:
-  i could choose different parts of the image and realign them differently (for ex. position one part more on the left, another part more on the right?)?
- eliminate a part of the image and replace it with a part of the image above?
- how can i save my realigned images so that they have the same name as before?

Thank you very much in advance!

[Saalfeld, Stephan]

Yes.  Please try the deformable alignment tool (Shift + T).  You place
some landmarks (Shift click) and drag them around.  This, like the
affine alignment tool is limited to the current selection.  You can
draw masks into selected patches (select (arrow tool, choose patches or
Ctrl A), draw a region of interest (e.g. ImageJ freehand tool), fill
with black (F)), you can copy individual patches, and you can send them
to other layers (both somewhere in the right click menu).  Using some
appropriate combination of these operations will enable you to do what
you asked.

Best,
Stephan


On Thu, 2016-04-14 at 09:57 -0700, inesica wrote:

> Hello everybody!
> I had a question about manual realignment with TrakEM2. I can align
> in x-y
> and also rotate, however I was wondering if:
> -  i could choose different parts of the image and realign them
> differently
> (for ex. position one part more on the left, another part more on the
> right?)?
> - eliminate a part of the image and replace it with a part of the
> image
> above?
>
> Thank you very much in advance!
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/help-w
> ith-TrakEM2-alignment-tp5016144.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[inesica]

Thank you very much! The deformable alignment tool helped me a lot. however,
when i export the images that i worked on, the one that i realigned seems
more blurry that the others (the second image in comparison with the
first)...is that normal?
<http://imagej.1557.x6.nabble.com/file/n5016149/image1-1.jpg>
<http://imagej.1557.x6.nabble.com/file/n5016149/image1-2.jpg>
thank you!




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View this message in context: http://imagej.1557.x6.nabble.com/help-with-TrakEM2-alignment-tp5016144p5016149.html
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[inesica]

Thank you very much! The deformable alignment tool helped me a lot. however, when i export the images that i worked on, the one that i realigned seems more blurry that the others (the second image in comparison with the first)...it's due to the re-sizing of the image and rotation, but is there any way to get better images while doing that?
thank you!

[Saalfeld, Stephan]

The deformed image is rendered by interpolation.  TrakEM2 uses bilinear
interpolation for export.  Your rendered image will have bands of
sharper and less sharp pixels depending on how close or far they fall
compared to the original pixels.  ImageJ's nearest neighbor
interpolator would preserve original pixels but lead to blocks and
aliasing.  ImageJ's bicubic interpolation would remedy the banding to
some extent but introduce halos.  We also have a Lanczos interpolator
in the pool that would also help with the banding and aliasing and also
introduce halos.  If there is true need to make this available in
TrakEM2's export, I am willing to add this as an option some time soon.
 But please first check how important it is really.

Thanks,
Stephan

On Fri, 2016-04-15 at 00:47 -0700, inesica wrote:

> Thank you very much! The deformable alignment tool helped me a lot.
> however,
> when i export the images that i worked on, the one that i realigned
> seems
> more blurry that the others (the second image in comparison with the
> first)...is that normal?
> <http://imagej.1557.x6.nabble.com/file/n5016149/image1-1.jpg>
> <http://imagej.1557.x6.nabble.com/file/n5016149/image1-2.jpg>
> thank you!
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/help-w
> ith-TrakEM2-alignment-tp5016144p5016149.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
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