We're in the process of testing out a 360 3D camera rig and getting pretty good results thus far, but I'm wondering if anyone knows of any good tutorials or guides on stitching. (Using Autopano Video Pro and Giga right now). I'm finding it a very powerful tool for automated stitching of multiple cameras, but where I hit a wall is trying to have some input on where it puts the stitch lines. For example, we have a lot of overlap between the equatorial stereo cameras and the mono nadir and zenith cameras, but Autopano tends to favor the nadir and zenith cameras, sometimes using them halfway to the horizon line. Obviously, we would prefer to favor the stereo cameras as much as possible and keep the mono cams to the necessary minimum, and there should be plenty of overlap to do so, but I have as yet been unable to find any control mechanism (or reference in the documentation) for controlling the location of stitch lines.
You might consider masking the unwanted areas of the zenith and nadir images. It should then only use the non-masked areas. Most algorithms and software for stitching don't take much in the way of pre-known knowledge from the user (basic lens info)