Stacks alignment

Hi all,
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.

Thanks,
Suman

Hi Suman

You need to use image registration for this.
Have you tried StackReg?
Using the Translation option should be enough.

Other options are listed here: https://imagej.net/Registration
These work well: Linear alignment with SIFT and Register Virtual Stack Slices (if you don’t want to load all images into memory)

Cheers
Pradeep

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And if you want to align vertically/horizontally pixel by pixel, manually you can use the Align_Slice plugin available here:
https://blog.bham.ac.uk/intellimic/g-landini-software/

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