Is there any form of plugin that can register two stacks to each other?
I use registration plugins to align stacks, and in these cases the plugin aligns each image in the stack to the previous image. The problem occurs with multi channel images where all channels were not acquired at the exact same timepoint. In those cases, I have perfectly aligned stacks in Z in the channels, but some of them will be offset in XY.
Is it possible to somehow match these stacks to each other based on the image data? There are structures that show upp in all channels that could be used for this purpose.