You can have a look at the following example papers and links:

XuvTools: free, fast and reliable stitching of large 3D datasets. Emmenlauer M, Ronneberger O, Ponti A, Schwarb P, Griffa A, Filippi A, Nitschke R, Driever W, Burkhardt H. http://www.ncbi.nlm.nih.gov/pubmed/19196411

C. Sun, R. Beare, V. Hilsenstein, and P.T. Jackway, Mosaicing of Microscope Images with Global Geometric and Radiometric Corrections. Journal of Microscopy, 224(2):158-165, November 2006.

http://vision-cdc.csiro.au/changs/doc/sun-etal06jmi.pdf

There is mentioning about a few packages in the XuvTools paper. Here are a few more softwares (partial list):

http://www.cs.bath.ac.uk/brown/autostitch/autostitch.html

http://filippopiccinini.altervista.org/Mosaicing/Mosaicing.html

http://hugin.sourceforge.net/

http://research.microsoft.com/en-us/um/redmond/groups/ivm/ICE/