I am having an issue regarding the image alignment. I tried to keep my sample as horizontal as possible while performing the scanning but still, there is a continuous lateral deviation in between each slice of my sample. I have a 16 cm diameter sample and want to crop it into 14 cm in diameter. The problem is I have a large number of samples and 800 slices for each individual sample. How can I align each slice one over the other so that I can crop all the stacks at once? Please refer to the image which shows the alignment difference between two extreme slices of my sample. I specified a region of interest of 14 cm diameter to one of the slices such that its parallel to the actual diameter of the slice but when I checked the same region of interest on the other slice, it is totally misaligned.