Complex systems, such as the brain, exhibit multiple levels of organization due to processes which support the separation of scales across time and/or space. That is, cooperative phenomena--or "modes" of activity--occurring at one scale give rise to coherent spatiotemporal structures at a coarser scale. In turn, structures at the coarser scale constrain--and hence influence--emerging activity at a finer scale. BrainModes is an annual scientific summit which seeks to bring together experimental, computational and theoretical neuroscientists engaged at different levels of organization, with the goal of advancing a principled approach to understanding brain function based on the concept of cooperative phenomena in complex systems. Phenomena of particular interest include synchronization, stochastic influences, and spatiotemporal processes in both healthy and pathological states such as seizures. This Special Issue reports the 2008 BrainModes Workshop, held in Amsterdam (December 2008) which focused on the application of this framework to the analysis of brain oscillations and synchronization phenomena across time scales.