Thanks for your interest. We do have segmentation of single cells. The current results, as used in integrated cells, are obtained by the method documented in the following page:
This was implemented in Matlab, not part of the new segmenter.
Meanwhile, we have developed a new deep learning based method for 3D cell/nuclei segmentation using our new segmenter. We haven’t publicly presented this method yet. The public release of these new methods is on our plan. Stay tuned 
For CellProfiler 3d, technically, all the classic image segmentation workflows as you have seen in our segmenter could be implemented as a CellProfiler 3D pipeline. We haven’t done so due to limited bandwidth.
Again, thanks for your interest. Let me know if you have more questions.
Jianxu