The logic is more complex than you have considered. Mice do a lot of exploratory behavior - nose in, nose out. Get half way in then back out. And of course you need to detect the mouse going the other way. Do you want to keep a separate count for each direction?
How far apart are the sensors? Can the mouse activate both sensors simultaneously or only one at at time? Can the bedding or food or other material (mice do leave other material behind) activate a sensor? Is there a time limit? What if the mouse goes to sleep at a sensor? Are there ever two or more mice in the enclosure at one time? how will you handle the case where two mice meet in the tunnel? Can they pass each other in the tunnel? What if four or five go through as a tightly packed group? Are there multiple tunnels?
When I have worked on animal tracking devices, I have found that a carefully drawn flow chart showing every possibility is very useful. You may be surprised at how complicated it can be with just two sensors. It is similar to the logic for interpretting a quadrature encoder for rotary motion.
Also your VI should have some kind of timing. The loop runs as fast as possible, limited primarily by the DAQ Reads. How fast do you expect things to happen? You could read the port and get the data as an integer rather than using two separate Reads. This would be more expandable when you decide to add more sensor pairs. Once you get this working, someone will want more sensors. They always do.
Lynn
