Unwarp edge of neural tissue stack.

[Ethan Cohen]

I have a z-stack of 2-D confocal images of neural tissue where the surface is slightly warped.

Is there some way to create a virtual rubber sheet of the surface, where a lattice of surface points are notated (zsection, x, y), and then transform the whole z-stack to align the surface flat?

Ethan.

Ethan Cohen, Ph.D.
Div of Biomedical Physics, WO62 Rm 1204
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[jerie]

Have you tried the unwarpJ plugin?
J.

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[Ignacio Arganda-Carreras-2]

Hello Ethan,

Do you think those points can be detected automatically? Maybe you can try
the Register Virtual Stack Slices plugin with the elastic transform or the
"moving least squares" solution:

http://fiji.sc/Register_Virtual_Stack_Slices

Cheers!

On Thu, Jan 21, 2016 at 11:30 PM, jens rietdorf <[hidden email]>
wrote:

> Have you tried the unwarpJ plugin?
> J.
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>



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[Saalfeld, Stephan]

Or you macrorecord/ script something with the transform landmark
correspondences plugin

http://fiji.sc/Landmark_Correspondences

But I have to admit that I have only a fuzzy understanding of what you
are looking for.  This and all previously suggested solutions are all
2D, i.e would warp individual slices of a 3D stack.  If you want to warp
the stack, you may want to have a look at John Bogovic's BigWarp

http://fiji.sc/BigWarp

better introduced in a talk at the ImageJ conference

https://vimeo.com/140929688

Best,
Stephan



On Fri, 2016-01-22 at 10:59 +0100, Ignacio Arganda-Carreras wrote:

> Hello Ethan,
>
> Do you think those points can be detected automatically? Maybe you can try
> the Register Virtual Stack Slices plugin with the elastic transform or the
> "moving least squares" solution:
>
> http://fiji.sc/Register_Virtual_Stack_Slices
>
> Cheers!
>
> On Thu, Jan 21, 2016 at 11:30 PM, jens rietdorf <[hidden email]>
> wrote:
>
> > Have you tried the unwarpJ plugin?
> > J.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>

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