The GIMP proved unsuitable to do what I wanted.
Instead I found a great program called ImageJ:
http://rsb.info.nih.gov/ij/
Basically it is a scientific program used to analyze images. It can count particles, pixels, you name it. The macro interface was extremely straight forward and I was able to process 2000+ images in less than a minute.
From there it was a simple matter of exporting the data to a text file and importing it into openoffice.org.
Very sweet little program!