The Cellular Annotation Tool
See the associated paper at: https://www.nature.com/articles/nbt.4225
The code in this repo is rather old by now. It was mostly written to run data analysis specifically for the above mentioned Nature article, as a proof of concept of DNNs for subcell localization predictions, and can therefore be somewhat hard to read in places.
If you are interested in annotating subcellular localizations, you should probably check out the newer, and better documented, Densenet model which has better performance than this model.