Optical coherence tomography (OCT) and Fourier domain intefereometry (OFDI) provides single micron image resolution of in vivo biological systems. This high speed multi-channel data acquisition system is capable of recording dual high speed optical channels at data sampling rates up to 1200 mega samples per second. Combining the disciplines of high speed analog amplifier design, filter design, analog to digital conversion design with low cost efficient FPGA design provides a cost effective data acquisition and data processing engine.