The proper approach to a project of this kind is careful thought, preparation 
and execution.

It is silly to expect to achieve good quality results by the post-hoc 
manipulation of imprecise or inconsistent  input data.

The easiest approach is to ensure that the images are taken from the same PoV 
with the same setup, and each series is stitched independently.
-----------------------------------------
An interesting possibility, for a project of this kind, would be a 
slideshow/series of crossfades between a sequence of panos taken as the light 
changes, or the seasons progress.

Take the image series from the same place... with the same lens and focal 
length... not neccesarily on the same day.

I'm happy to share a little JavaScript blob that accomplishes 
crossbrowser/crossfade transitions, with anybody that wants it.

It works at... http://www.w3a2z.net/Rasha/ 

John

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