Tuolomee AUV's software is what allows it to operate autonomously. It is structured around Robot Operating System (ROS). A state machine controls each individual task which the robot has to complete. All movement is controlled by a series of proportional, integral, derivitive (PID) controllers, which use data from all of the sensors to determine how fast each thruster needs to move in order to accomplish the goal of each individual task. To the right, see a flow chart of system functionality. The AUV's decision making is dependent on many things including depth, image vision, and many more.

Pictured: AUV decision making flow chart