initial commit of this file.. basic functionality currently broken because i'm using a different stitching algorithm for calculating images to register than i want to use to ressemble the images.. old algorithms runs through python and fiji, new one will work through FijiBento style java module that calls the same code.. but the rendering is done in slightly different ways, due to version issues in stiching i think.
initial commmit of other code
REMOVING THIS JAR
removing this file
connected new stitching module up
added reconstruction dependancies