Extended Data Fig. 9: TC and CT projection patterns and rules between reciprocally connected areas.

a, Schematic summarizes observed projection patterns between core thalamic nuclei (blue circle) and their reciprocally connected cortical targets (L1–L6 colour coded). Laminar patterns are from Fig. 5g. STPT images of labelled axon terminals between three pairs of core nuclei and primary sensory cortex that perfectly follow rules in both directions. In the FF direction (LGd to VISp, VPL to SSp-ll, VPM to SSp-n), projections are dense in L4 or L4 and L6 (clusters 4, 8). In the FB direction, CT projections predominantly arise from L6. b, Schematic summarizes observed projection patterns between matrix-focal thalamic nuclei (orange circle) and their reciprocally connected cortical targets. STPT images of reciprocal connections between PT and ILA, MD and ORBl, and MD and AId illustrate the schematized rules. Projections from these thalamic nuclei belong to clusters with relatively fewer L1 axons (FF-like, clusters 3, 7, 9). The reciprocal CT input is also stronger from L6 (FB), like the core nuclei above. c, Three schematics are shown to summarize observed projection patterns between matrix-multiareal thalamic nuclei (red circles) and their reciprocally connected cortical targets. The top schematic shows dense TC projections to L1 (FB) with CT projections originating from L5 (FF). The middle schematic (with relevant example images boxed) shows reciprocal connection patterns in which TC projections target mid-layers (FF-like) and the reciprocal CT input is stronger from L6 (FB). The bottom schematic shows the same TC projection pattern as the top schematic, but with CT projections originating approximately equally from L5 and L6. STPT images show reciprocal connections between multiarea-matrix thalamic regions LP, PO, RE, and VM to three cortical targets each. Some regions have target-specific projections that are either FF or FB. For example, different from the LP-to-VISp projection (FB), axons from LP to VISam and ACAd target mid-layers as opposed to L1 (clusters 8 and 5, FF), and the reciprocal connection arises more from L6 (typical for FB). Projections from PO, RE, and VM to all three cortical targets are consistent with a FB projection (denser terminations in L1 and either L5 or L6 (clusters 2 and 6). Reciprocal CT projections originate from L5 or, both L5 and L6. We did not see CT input arising equally from both layers or more from L5 when the reciprocal TC projection was considered FF, consistent with the ‘no-strong-loops’ hypothesis³⁷. All panels: overall, FF projections from core thalamic regions are in clusters 4 and 8. FB projections from matrix-multiareal thalamic regions are in clusters 2 and 6, like CC FB. The matrix-focal results support the notion that patterns with relatively less L1 involvement (3, 5, 7, 9) are FF, particularly given the strong reciprocal input observed from L6. STPT images are from the approximate centre of the axon termination field for each target region. Cortex images were rotated so that the pial surface is at the top. Cluster assignments (for TC) are indicated in each panel. Text labels above image show FF and FB direction based on relative position in Fig. 6. Dashed lines indicate region borders.