Thanks for the awesome suggestions. I have converted all the files by hand but I still have the problem of stitching them all together.
I have given Fiji a good go but have not had any success. Pic of error and settings: http://i1182.photobucket.com/albums/x445/Four_Leaf_Clov/Errorandsettings_zps7b25075b.jpg I have tried doing what imageJ's website suggests, but I cannot get it to work. I have used the Positions from File part of the stitching plugin however the program does not display an image or write to disk after the calculations. Any ideas on what might be going wrong?
I also tried ICE but it seems incapable of stitching together so many files ( it arranges everything perfectly but drops 80% of the tiles, leaving a grey area in the mid
I feel like this is more difficult than it should be.