I have 3D+T label maps generated by a different tool. Is it possible to use 3DCT on a segmentation output from a different software/tool for tracking?

It's possible to do that in principle, and it would be even better if you had accurate segmentation results for all frames, but as of now the current version of 3DeeCellTracker doesn't have a function to utilize the segmentations from other tools. Hopefully, I'll be able to add that feature in the future when I have more time.