(a–f) Calcium binding proteins and neuropeptides (green) were used to visualise specific interneuron populations in the cortex, showing labelling patterns of calbindin (CB; a) calretinin (CR; b) parvalbumin (PV; c) and neuropeptide Y (NPY; d) somatostatin (SOM; e) and vasoactive intestinal peptide (VIP; f) populations in 20 week WT cortex stained with DAPI (blue) and Nissl (red). The boxed areas (a–f) in the high magnification images show co-localisation of interneuron labels with Nissl stain. (g,h) At 20 weeks, analysis of motor cortex, reveals the normal distribution of CR-interneurons in WT motor cortex (g) but a striking reduction in particular in layers I-IV of SOD1G93A motor cortex. (h) Analysis of immunopositive neurons within the SOD1G93A motor (M) and somatosensory (S) cortex showed that the density of calretinin-expressing interneurons was significantly decreased specifically within the supragranular (Ms, layers I-IV) lamina of the motor cortex (j) and the density of Neuropeptide Y-expressing interneurons was significantly increased in both the supragranular (Ms, layers I-IV) and infragranular lamina (Mi, layers V-VI) of the motor cortex. (l) No other interneuron populations were significantly altered in either motor or somatosensory cortex. (i,k,m,n) Values in graphs represent means ± SEM. *P < 0.05, two-way ANOVA, Bonferonni’s multiple-comparison test with n = 6 mice per group. Scale bar in (a–f) 20 μm, (g–h) 100 μm.