Re: 3D Unwarp a tissue of fixed thickness in z direction
Posted by
Glen MacDonald-2 on
Apr 10, 2017; 11:53pm
URL: http://imagej.273.s1.nabble.com/3D-Unwarp-a-tissue-of-fixed-thickness-in-z-direction-tp5018496p5018498.html
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
(206) 616-4156
[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?
>
>
>
>
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