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I did use the same mRuby2 construct from addgene, and like you started and the 
normal GFP start site. I just rechecked the sequence too and everything looks 
perfect. I am setting up to test it again on the 2-photon. Part of the issue may 
be the filter I am using (565-610), which is probably not far enough red to be 
optimal, but should catch over half of the signal. What filter do you use?

Steve