Hi all-
I am brand new to ImageJ/Fiji, but have spent a little bit of time
exploring the registration plugins available. I'm not sure if I have yet
found what I need for the following problem:
I have Z stacks obtained over time. Each Z-stack does not need
registration, but I do need to register the Z-stack from T=1 with the Z
stack from T=2, and the Z stack from T=2 with Z stack from T=3, and so on.
Because I am obtaining these Z stacks over long periods of time in an
automated fashion, the Z-stacks are not 100% aligned with each other, but
they are pretty close. Each Z stack will start at a slightly different
focal plane, and there is a small amount of X-Y misalignment as well.
I had tried MultiStackReg, which certainly will align one Z-stack with
another, but it doesn't consider different focal planes - it aligns slice 1
from one stack with slice 1 from the other stack.
Is there a plugin that can handle the task above? If so, can it handle very
large files (i.e. feeding in a large stitched Z-stack grid from T=1 to
align with a large stitched Z-stack grid from T=2)?
Thanks so much for your help!
-Jason Miller
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Jason Miller, MD, PhD
University of Michigan Kellogg Eye Center
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