The aim of computational neuroscience is to gain insight into the dynamics and functionality of the nervous system by means of modeling and simulation. Current research leverages the power of High Performance Computing facilities to enable multi-scale simulations capturing both low-level neural activity and large-scale interactions between brain regions. In this paper, we describe an interactive analysis tool that enables neuroscientists to explore data from such simulations. One of the driving challenges behind this work is the integration of macroscopic data at the level of brain regions with microscopic simulation results, such as the activity of individual neurons. While researchers validate their findings mainly by visualizing these data in a non-interactive fashion, state-of-the-art visualizations, tailored to the scientific question yet sufficiently general to accommodate different types of models, enable such analyses to be performed more efficiently. This work describes several visualization designs, conceived in close collaboration with domain experts, for the analysis of network models. We primarily focus on the exploration of neural activity data, inspecting connectivity of brain regions and populations, and visualizing activity flux across regions. We demonstrate the effectiveness of our approach in a case study conducted with domain experts.