3D Unwarp a tissue of fixed thickness in z direction

[Ethan Cohen]

I have a thin neural tissue of fixed thickness which after histo processing you can think of as a slightly bent cheddar cheese slice.

Now I confocally reconstruct the bent cheese slice as a series of Z sections in an image stack.  I know where the x,y position on the surface of each part of the cheese slight starts in the Z-stack, but these x,y positions are not all on a single Z-section.

Now I want to align the Z-stack (by vertically adjusting the lines of Z pixels) so the 3-D image of the cheese slice is flat, and each x,y  position on the surface starts in a single z section.

Can ImageJ/Fiji do this? Define some sort of mesh?

Elastix?




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[Glen MacDonald-2]

Dear Ethan,
Have you tried a  simple Projection based on Maximum Intensity, summed intensity or average intensity, or the Extended Depth of Field plugin?

Glen MacDonald
Digital Microscopy Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
[phone]
[hidden email]

> On Apr 10, 2017, at 2:41 PM, Cohen, Ethan D <[hidden email]> wrote:
>
> I have a thin neural tissue of fixed thickness which after histo processing you can think of as a slightly bent cheddar cheese slice.
>
> Now I confocally reconstruct the bent cheese slice as a series of Z sections in an image stack.  I know where the x,y position on the surface of each part of the cheese slight starts in the Z-stack, but these x,y positions are not all on a single Z-section.
>
> Now I want to align the Z-stack (by vertically adjusting the lines of Z pixels) so the 3-D image of the cheese slice is flat, and each x,y  position on the surface starts in a single z section.
>
> Can ImageJ/Fiji do this? Define some sort of mesh?
>
> Elastix?
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Ethan Cohen]

Glen:

We tried many types of Z-projection in ImageJ/Fiji, and have written macros for them.
What we need to do is make the cheese slice of sectionned tissue flat, preserving the z-information in the thin slice, just shifting columns of data up or down between stacks so that the surface of the slice is all in one Z-frame.

Ethan.


Ethan Cohen, Ph.D.
Div of Biomedical Physics, WO62 Rm 1204
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-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Glen MacDonald
Sent: Monday, April 10, 2017 7:54 PM
To: [hidden email]
Subject: Re: 3D Unwarp a tissue of fixed thickness in z direction

Dear Ethan,
Have you tried a  simple Projection based on Maximum Intensity, summed intensity or average intensity, or the Extended Depth of Field plugin?

Glen MacDonald
Digital Microscopy Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
[phone]
[hidden email]

> On Apr 10, 2017, at 2:41 PM, Cohen, Ethan D <[hidden email]> wrote:
>
> I have a thin neural tissue of fixed thickness which after histo processing you can think of as a slightly bent cheddar cheese slice.
>
> Now I confocally reconstruct the bent cheese slice as a series of Z sections in an image stack.  I know where the x,y position on the surface of each part of the cheese slight starts in the Z-stack, but these x,y positions are not all on a single Z-section.
>
> Now I want to align the Z-stack (by vertically adjusting the lines of Z pixels) so the 3-D image of the cheese slice is flat, and each x,y  position on the surface starts in a single z section.
>
> Can ImageJ/Fiji do this? Define some sort of mesh?
>
> Elastix?
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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