Brian Long

the intended specification for the codebook included non-integer values, but the current implementation uses integers when creating the `Codebook` object from a .json file. Non-integer values already work as desired...

registration in starfish, Part 3: implement image / spot registration in IntensityTable

2

A potentially very useful aspect of the `IntensityTable` as a data structure for pixel intensities is that it provides an alternative location to execute (approximate*) rigid image transformations. Instead of...

registration in starfish, Part 1: zero out wrapped values

6

The lone registration module `fourier_shift` [uses](https://github.com/spacetx/starfish/blob/berl-zero-wrapped-intensities/starfish/pipeline/registration/fourier_shift.py) scipy's [ndimage.fourier.fourier_shift](https://docs.scipy.org/doc/scipy-0.15.1/reference/generated/scipy.ndimage.fourier.fourier_shift.html), which wraps intensity values from one side of the image to the other. I've tried to fix this by tacking on some...