Changing Z axis

Posted by scgallant on Jun 12, 2017; 5:31pm
URL: http://imagej.273.s1.nabble.com/Changing-Z-axis-tp5018880.html

Hello,

Apologies if this question has been posted before, have not been able to find the answer...
I have a stack of 2D images, taken of slices and registered by x/y fiducials that represent the true Z axis.
I am looking for a way to define a new Z axis while keeping the interslice relationships created by registration/alignment; basically want to pick an X/Y coordinate on each slice and create a new z axis around that coordinate, as if I was taking the 3D stack I created and tilting it, so as then to reslice it into 2D images with the new Z axis.

Basically problem created by making histology slices which are close to but not quite aligned with the z-axis around which I want to make angular measurements.

Help greatly appreciated - thank you.

-Sara