Fix to subplots, initial shift in register now 3d, fix to unit tests, removal of redundant code, fix to rounding errors in auto thresh

[reillytilbury]

Checklist

• [ ] I have updated the changelog.txt, if applicable.
• [ ] I have bumped the software version in _version.py, if applicable.
• [x] I have checked that the unit tests passed.
• [x] I have checked that Minnie and/or RoboMinnie passed.
• [x] I have resolved merge conflicts.

[paulshuker]

Great as long as the numpy array is some kind of float type it should pass