We are happy that Professor Dogariu has taken such interest in our Viewpoint and took the time to react to it, and would like to thank him for his comment. We welcome his suggestion to cite two papers to provide the readers with some additional background on this topic.
In an excellent and visionary paper, Freund  suggested that for a disordered system one could effectively use measured correlation functions and reference patterns as optical elements. Indeed, he even determined the optical resolution that can be attained in such a system. In most of these applications, implicit knowledge of the transmission matrix is used. Freund even predicted that explicit measurements of the transmission matrix could possibly be used to eliminate the use of reference patterns. We agree Freund’s paper is an important part of the historical context of the measurements of the transmission matrix.
Professor Dogariu further suggests the in-depth review by van Rossum and Nieuwenhuizen . One of us has made a small contribution to this work, and we are very proud that it is considered an important paper in the field. We have not tried to completely review the field of optics of complex materials, but let us take this opportunity to recommend some excellent reviews: the very informative new book compiled by Noginov et al.  contains chapters written by top scientists. Beenakker  also reviews theoretical parallels between condensed matter systems and photonic systems. The book compiled by Sebbah  has already become a classic and contains many applications as well as basic theory.
Almost all work in the field makes use of the transmission matrix, explicitly or implicitly. In our Viewpoint commentary we focused on the new opportunities that are opened by having explicit knowledge of a sizable fraction of the transmission matrix, and we have therefore concentrated on work that already uses such knowledge, and areas we expect to be most transformed by having direct access to the matrix elements.
- I. Freund, Physica A 168, 49 (1990).
- M. C. W. van Rossum and T. M. Nieuwenhuizen, Rev. Mod. Phys. 71, 313 (1999).
- Tutorials in Complex Photonic Media, edited by M. A. Noginov et al. (SPIE Press, Bellingham, 2010)[Amazon][WorldCat].
- C. W. J. Beenakker, arXiv:0904.1432 (2009).
- Waves and Imaging through Complex Media, edited by P. Sebbah (Kluwer Academic, Boston, 2001)[Amazon][WorldCat].