Fig. 1

Cre-driver mice label specific pyramidal neuron types. a, b Coronal images of injection sites in Tlx3_PL56 (L5-IT) and Sim1_KJ18 (L5-PT) show somata locations. Scale, 0.5 mm. c Somata locations of Sim1_KJ18 mice injected in vM1, fM1, and S1. Comparison at right. N indicated shows # of sections (# of mice). Purple, vM1; burgundy, fM1; teal, vS1. Pia is relative laminar depth of 0; white matter is 1. Error bars represent SEM. Red tick marks show estimated cortical layers. d Mean somata distribution for lines labeling L2/3 (Sepw1_NP39), L5-IT (Tlx3_PL56), L5-PT (Sim1_KJ18), and L6 (Ntsr1_GN220). e Targets of IT-type (Tlx3_PL56) and PT-type (Sim1_KJ18) neurons, illustrated with single-axon reconstructions. IT-type neurons (blue) project to ipsi- and contralateral cortex (Ctx) and striatum (Str). PT-type neurons (gold) target ipsilateral cortex, striatum, and subcortical targets in thalamus (Thal), superior colliculus (SC) and brainstem. f–h Image of Sim1_KJ18 injection site. White box in f indicates magnified area (g, h). Scale 0.5 mm. h Annotation of somata in Neurolucida. Blue circles indicate AAV-infected cell bodies expressing smFPs. i, j Coordinates of somata and fiducial markers placed along pia and white matter of cortex were aligned to the CCF. Somata for three injections (teal, burgundy, and purple) and fiducial markers (gray) were then plotted in 3-d (1 mm scale). Rotated projection (j) shows dorsal view of injection site center of mass (teal) and anterior/posterior spread of infection. (k) Injection site center of mass of Tlx3_PL56 (N = 92, circles) and Sim1_KJ18 (N = 62, triangles) plotted and spatially clustered. Eight clusters shown in red (M2), orange (ALM), purple (vM1), burgundy (fM1), green (llM1), yellow (fS1), teal (vS1), and gray (orfS1). Indeterminate injection sites are black. Sites are superimposed on an image of the dorsal surface of mouse cortex. Black cross marks midline and bregma. Scale, 1 mm