I am not sure I understand exactly what you are trying to accomplish since pixels labeled with a zero value report background not branches. Branches are labeled with integers starting from 1. But here are some pointers that hopefully will help. Do let us know if not otherwise:
- You can edit the LUT color assigned to zero using Image>Color>Edit LUT... by editing the first entry in the LUT ramp
- You can segment any desired order in the Sthraler mask image: Specify desired value(s) in the Set... prompt of the threshold widget, then press "Apply".
- If chosen, the iteration stack option will already display individual branch orders