After a week of debugging I got the code to do what I wanted.  I have successfully detected a bit stream in the chessboard marker image.  I had to correct for a small error that I encountered las week that was related to the hard color values that I was using.  I changed the code so that now I am using a dynamic color range.  The range is created with known colors in known positions.  With this range I can adjust to specific image characteristics.

After I killed the last bug in my code I went ahead and took pictures in different lighting setups.  The algorithm correctly detected all the colors in the marker in all the pictures.  I have to further test with outdoors lighting to see if it affects the algorithm at all.  I’ll be doing this in the coming days.

There is still a lot to do to get this to work with our Biologists collaborators:  1. There needs to be a part of the application that creates the chessboard markers;  2. There needs to be a semi-decent GUI to initialize the picture analysis process;  3. The part of the application that takes care of differentiating the images does not exist; 4. We could code stuff in a more efficient way. Though these four things are currently lacking, they are the least of my worries.  The algorithm that detects the marker works; the rest is icing on the cake.

You can get the code here.  I currently do a very crappy job at describing how to use the code.  This will also improve in the coming weeks. :)