  The fly tracking software Ctrax by Branson et al. is popular for positional
tracking of animals both within and beyond the fly community. Ctrax was not
designed to handle tracking in difficult lighting conditions with strong
shadows or recurring "on"/"off" changes in lighting - a condition that will
likely become increasingly common due to the advent of red-shifted
channelrhodopsin. We describe Ctrax extensions we developed that address this
problem. The extensions enabled good tracking accuracy in three types of
difficult lighting conditions in our lab. Our technique handling shadows relies
on "single animal tracking"; the other techniques should be widely applicable.
