I collected 3D confocal images by slice-by-slice raster scanning. Since the scanning may take pretty long (30 min), there is frame-to-frame drift. I am wondering if there is a way to correct for this kind of drift? I know Correct for 3D drift fiji plugin, but my data is 3D, not 4D. It is not time lapse. So it is not what I need. I appreciate any suggestions. Thank you.
I guess your data is time lapse It is 2D time lapse while changing Z depth position, with time allowing for messing in the x-y direction of every slice. Why not correct for drift in 2D, considering Z as time (x,y,t), then consider the corrected image as 3D (x,y,z)?
Stackreg and Turboreg plugins come to mind.
Start in the Z-middle of your stack.