A flow cell assembly for measuring the flow rate of gas in a pipe having an optical probe mounted on a flow cell inserted between sections of pipe. A distal end of the optical probe is disposed within an internal bore of the flow cell. The optical probe is capable of measuring the velocity of particles in a gas flowing through the internal bore. A sensor mechanism may be mounted on the flow cell and have a sensor array with a distal end disposed within the flow cell internal bore. The sensor array is capable of measuring physical properties of the gas. The optical probe is self-aligned when mounted to the flow cell through the use of a locking cam and an orientation ring. Velocity and physical property measurements are used to calculate flow rate. Alternatively, the optical probe and sensor mechanism may be mounted directly onto an existing pipe.