20180109 Image Alignment and Registration notes
For image alignment or registration, today we tried all the plugins bundled with Fiji and found one that works.
The following worked perfectly with Fiji 1.51s Java 1.7 20180109 on a stack of 16 bit grayscale images where there was information across the entire field, but failed with synthetic 8 bit image with a lot of black space. We like thatthe xml files appear to have the offsets used for the corrections so they may be applied to other channels or images (but we haven't tested it).
For single channel stacks, this has been the method we've used for years:
http://bigwww.epfl.ch/thevenaz/stackreg/ and http://bigwww.epfl.ch/thevenaz/turboreg/ with discussion why separate fro Fiji here http://forum.imagej.net/t/stackreg-and-turboreg/5887
You don't see them here, but in this directory we have stored the versions that work with ImageJ 1.51s Java 1.8 for Windows 64bits (not Fiji) as of 20180109 and are available by request if for some reason you cannot get the official versions linked above.