Neural microcircuits are the computational units of the mammalian brain. Recent evidence suggests that they are not composed exclusively of neurons but also involve other cell types such as astrocytes and microglia. In the healthy brain microglia, the resident immune cell, closely interacts with synapses and is likely to be involved in their structural plasticity. The interaction between the nervous and the immune systems is even more prominent under pathological conditions such as brain injury, inflammation and neurodegenerative diseases. This review discusses the techniques for high resolution imaging of microcircuit function in health and disease by focusing on some of the most recent advances in the field of in vivo calcium imaging of neurons, astrocytes and microglia.