We study the degrees of freedom of optical systems and signals based on space-frequency (phase space) analysis. At the heart of this study is the relationship of the linear canonical transform domains to the space-frequency plane. Based on this relationship, we discuss how to explicitly quantify the degrees of freedom of first-order optical systems with multiple apertures, and give conditions for lossless transfer. Moreover, we focus on the degrees of freedom of signals in relation to the space-frequency support and provide a sub-Nyquist sampling approach to represent signals with arbitrary space-frequency support. Implications for simulating optical systems are also discussed. © 2013 Optical Society of America.