Alejandro

[Mossi8]

Few minor changes:

1. Segmentation saved again as zarr files seemed to work.
2. Split processing_fresh_nuclei (def processing_assign_dots, added to run_full) last step of register_assign function because it crashes after create_label, but it completes it.
3. Seems like when the registration of 40X nuclei has big shifts, they tend to be removed of this function of stitching_graph_fresh_nuclei:
   '''all_registrations_removed_large_shift = {
   k: v for (k, v) in all_registrations_dict.items() if np.all(np.abs(v[0]) < 20)
   }'''
   which I changed to:
   all_registrations_removed_large_shift = {}
   for (k, v) in all_registrations_dict.items():
   if np.all(np.abs(v[0]) < 20):
   all_registrations_removed_large_shift[k] = v
   else:
   all_registrations_removed_large_shift[k] = [np.array([0,0]), 1.0]
   otherwise, the global_shift it too big
4. Add reprocessing option to processing_fresh_nuclei