Hi Ken!
Glad there is only one question now - or none at all.
With a "regular' panorama it makes sense to choose an adequate center for the image, say, pointing North or to some interesting feature in the image. However, panning the panorama in a viewer (standalone or through an internet page) you could see anywhere you want.
For your rectangular image, a mosaic of microscope photos, how will you see or present it to others? Using an image editor like Gimp, or maybe OpenSeadragon to show (efficiently) a very high resolution image in an internet page? In both cases the image will be presented centered in the window, scaled for best fit. The center will ever be the center of the image (or viewing window), and you could pan and zoom without difficulty. There is no need to define a center for your image!
Hope this makes sense,
Luís Henrique