Hi, I have been trying this for some time now, but can’t really get it to work.
At our lab, we produce confocal 4D data, i.e., stacks collected over time. Since this is in vivo data we get a lot of movement while acquiring it, both within stacks and drift over time. Using FIJI/ImageJ, I can correct movements in a stack. I can also (if i flatten the stacks) correct for movements over time. I have multi channel images and use the plugin multistackreg. The algorithms this plugin uses works very nicely for correcting the movements in our data!
What I want to be able to do is to correct for movements first in the stack at each timepoint, and then correct the stacks over time (i.e. in 3D).
Is this possible? To me (who can’t program) it feels like the functionality is there but just not setup up in a way that makes this possible to do at the moment.
Is anyone else doing this, or know of anyone that does?