Functional connectivity within cortical networks has traditionally been investigated by measuring the cross-correlation between the spike trains of pairs of neurons (Douglas et al., 1989 and Douglas and Martin, 1991). Still, little is known about functional

connectivity under sensory stimulation or about the role of inhibition in the cortical network. We combine multiple computational approaches with optogenetic activation of PV+ neurons to determine how inhibitory activity modulates network connectivity within and across layers and columns of the cortex. We targeted expression of the light-sensitive Erastin channel channelrhodopsin-2 (ChR2) to PV+ neurons in the mouse auditory cortex (Figure 1A), using a Cre-dependent adeno-associated virus (Sohal et al., 2009). One month posttransfection, we recorded neural responses with a 4 × 4 polytrode in putative L2/3 through L4 of the primary auditory cortex (Figure 1B) while playing pure tones to the contralateral ear and stimulating PV+ cells with blue light (Figure 1C). Functional connectivity between the recorded sites Osimertinib in vivo was quantified using Ising models, which

have previously been used to model neural interactions in many different systems (Ganmor et al., 2011a, Ganmor et al., 2011b, Köster et al., 2012, Marre et al., 2009, Ohiorhenuan et al., 2010, Roudi et al., 2009a, Schaub and Schultz, 2012, Schneidman et al., 2006, Shlens et al., 2006, Shlens et al., 2009 and Tang et al., 2008). The Ising model describes the coupling (a measure of functional connectivity) between pairs of recording sites and between recording sites and external stimuli based on observed population firing patterns and corresponding stimuli (Figures 1B and 1C). Because all pairwise interactions are fitted simultaneously, Ising models are less prone to false-positive interactions

that are inherent to traditional correlation analysis (Schneidman et al., 2006). For example, in a MTMR9 fully connected Ising model (see Experimental Procedures), the strongest coupling to sounds occurred in rows 3 and 4 (Figure 2A), corresponding to the thalamorecipient layers. By contrast, traditional correlation analysis indicated strong connectivity between sounds and sites in all rows (Figure 2B). This false-positive connectivity between sounds and activity in rows 1 and 2 is due to the absence of site-to-site interactions in the correlation analysis. In a reduced Ising model where recording sites were coupled to sound but not to each other, which we call the independent neurons model, positive couplings between neural activity and the sound stimulus were also present in all recorded layers and did not differ across depth (Figure 2C; p = 0.55, Kruskal-Wallis analysis of variance [ANOVA]).