A central question about the brain is how information is processed by large populations of neurons embedded in intricate local networks. Answering this question requires not only monitoring functional dynamics of many neurons simultaneously, but also interpreting such activity patterns in the context of neuronal circuitry. Here, we introduce a versatile approach for loading Ca(2+) indicators in vivo by local electroporation. With this method, Ca(2+) imaging can be performed both at neuron population level and with exquisite subcellular resolution down to dendritic spines and axon boutons. This enabled mitral cell odor-evoked ensemble activity to be analyzed simultaneously with revealing their specific connectivity to different glomeruli. Colabeling of Purkinje cell dendrites and intersecting parallel fibers allowed Ca(2+) imaging of both presynaptic boutons and postsynaptic dendrites. This approach thus provides an unprecedented capability for in vivo visualizing active cell ensembles and tracing their underlying local neuronal circuits.