How can I save the binary label maps for each class I segmented? Or is it possible to output multi-color segmentation label map?
By default (if segments don’t overlap) the segmentation that you save (.seg.nrrd file) is a multi-color segmentation label map.
If you want to have each segment in a separate volume then you can show one segment at a time and use “Export to files…” feature in Segmentations module with the “Visible segments only” option enabled.
You can also use slicerio Python package to load a .seg.nrrd in any Python environment, get the list of segments and any segment or combination of segments as numpy arrays.