The ICE auto alignment and fill in features are impressive and super cool. Still, I like MapKnitter since it lets you zoom in/out. I think that's really important since microscope lenses force you to pick between resolution or field of view. Once you make the mosaic you can have both by scrolling thru the image. Of course, you could probably do the same thing with an ICE Image by adding a separate viewer.
Right now, I am trying to compare different stitching programs to see how they work. My list so far is MapKnitter, ICE, ImageJ, Adobe photomerge and opencv stitcher. If you know of any reviews that compare performance of different stitching programs I would be interested. Thanks again for your help.
Also added some more frames to the initial mapKnitter post so you can see more of the bee leg.