I just got word from a friend of mine who's in the last throes
of his Ph.D. at local Max Planck that one of the guys in his group
is an active user of a free software (for Linux) which is used
to create 3d reconstructions of some critter (D. discoideum, I believe),
and that it only needs few manual touches, when it bungles the
segmentation. So it would seem to save a large amount of footwork.
While I have a day job that keeps me on the heels, I'll try to
take a day or two off, and ask the guy to show me what it can
do, and whether we can use it for our purposes.