Registration based on ROI content

Dear all,

I am looking for a way to register stacks. However, I want to be able to use an ROI to choose what I want the reference for registration to be (e.g. a fluorescent bead I have in the field, a speck of dirt, a specific cell).
Is there an existing solution for this already?
I just can’t find it.

Thanks for any help,


Hi Rafael,

If you need to register multiple 3D stacks to each other, you could give Atlas Toolkit a try:

You can define an ROI for each stack using the Segmentation Editor plugin, then register the resulting .label files together using Label Registration 3D. You can then apply the resulting registration parameters to the original stacks.



Hi Tim,

Thank you very much for the answer.
The Atlas Toolkit looks great.
However, I was hoping to not increase the number of steps too much. Adding a manual segmentation step would go against that goal.

I may have found a solution for my problem with the Correct 3D Drift script:

It seems to now work with 2D datasets as well. More importantly, “if a ROI is put on the image, only this part of the image is considered for drift computation, the ROI is moved along with the detected drift thereby tracking the structure of interest”. So I can make an ROI on my landmark and correct for only its drift.