Thomas J. Naughton focuses on Optics, Digital image processing, Encryption, Digital holography and Holography. His work in Optics covers topics such as Algorithm which are related to areas like Empirical modelling and Selection. He interconnects Speckle noise and Set in the investigation of issues within Digital image processing.

His work is dedicated to discovering how Encryption, Key are connected with Telecommunications and Cryptography and other disciplines. Thomas J. Naughton has included themes like Quantization, Computer vision and Artificial intelligence in his Digital holography study. The study incorporates disciplines such as Digital imaging, Digital image, Computer graphics, Compositing and Image formation in addition to Holography.