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The development of genetically modified mice in which subpopulations of cortical neurons are labelled by fluorescent proteins has greatly facilitated single-cellular imaging and electrophysiology studies in vitro and in vivo. However, the parallel visualization of both inhibitory and excitatory neocortical neurons remains problematic. We here provide an alternative approach to identify GABAergic neurons in the context of in vivo calcium imaging. The method relies on the Emx1(IREScre) recombinase driven expression of a red fluorescent protein in excitatory neurons and glia. We quantitatively examined the upper layers of the visual neocortex in vivo and found that due to pronounced neuropil staining Emx1(IREScre)-negative and Emx1(IREScre)-positive neurons can be reliably differentiated based on negative and positive contrast, respectively. Immunohistochemical analyses confirmed that the entire population of GABAergic interneurons is represented by Emx1(IREScre)-negative cells. The potential usefulness of the method is exemplified by calcium imaging of sensory-evoked responses in the primary visual cortex. We conclude that the proposed method extends the repertoire of strategies aimed at discriminating two major neocortical neuron populations in situ.