3D Unwarp a tissue of fixed thickness in z direction

Posted by Ethan Cohen on Apr 10, 2017; 9:41pm
URL: http://imagej.273.s1.nabble.com/3D-Unwarp-a-tissue-of-fixed-thickness-in-z-direction-tp5018496.html

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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