putting together microscope photos

I'm a summer student at aresearch lab. I am using the Zeiss Axiovert
S100
(http://kugrserver.health.unm.edu:16080/microscopy/_images/Ins3.jpg)
inverted microscope and the Zeiss Axiocam to take pictures of brain
tissue at 10x magnification. These are 1312x1030 pixel JPG pictures.
The
images were taken from left to right sequentially. So the whole image
is a grid of smaller images that has 40 rows with 8 images per row. I
would like to combine all of these pictures by merging their
overlapping regions. Is there a convenient way of doing this with any
stitching programs? Can MatLab do this? I'm looking for freeware or
trial versions. I do have Photoshop CS.

Thanks

.

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