As cockpit technologies advance and increase information-rich content is provided to aircrews, and it is possible that we are reaching the cognitive limits of the human operator. With additional layers of automation, crew alertness becomes equally important as high levels of workload. Foundational tools, methods, and technology components to quantitatively assess cognitive limits and to characterize operator state are needed to improve aircraft safety and enable full realization of the Next Generation Air Transport System (NGATS). Over the last two years, we have built up a neural imaging capability onboard our Computerized Airborne Research Platform (CARP) research aircraft, a Beech Bonanza. A similar system shall be deployed on the National Research Council (NRC, Canada) Bell 412 Advanced Systems Research Aircraft (ASRA). Flight trials on the ASRA are slated for November, 2006. We have collected preliminary physiological data using the CARP in flight to demonstrate that minute EEG signals can in fact be collected in the ecologically valid context of real flight. A secondary goal of our work was to develop data synchronization and artifact removal methods. In future research, we hope to automate these methods and collect physiological data to develop sophisticated Operator State Classification and Feedback models. This research program is a collaborative effort between the National Research Council Canada and the Operator Performance Laboratory (OPL).