Extended Data Fig. 4: Representative images of presynaptic inputs to the visual areas from anatomical structures outside of cortex and thalamus.

Coronal STPT images and their corresponding 2D atlas plates in Allen CCFv3 show labeled presynaptic neurons in OLF (a-a’), HPF (b-b’), CTXsp (c-c’), STR (d-c’), PAL (e-e’), HY (f-f’), MB (g-g’), pons (h-h’), and MY (i-i’). Claustrum (CLA) in CTXsp, diagonal band nucleus (NDB) in PAL, and lateral hypothalamic area (LHA) in HY each represent ~0.1% of whole brain inputs; globus pallidus, external segment (GPe) in PAL, basolateral amygdalar nucleus (BLA) in CTXsp, and zona incerta (ZI) in HY each account for ~0.01% of whole brain inputs; dorsal peduncular area (DP) in OLF, locus ceruleus (LC) in pons, and superior colliculus (SC) in MB each account for ~0.001% of whole brain inputs; areas in MY each account for ~0.0001% of whole brain inputs. Rare inputs in several structures of MY are also found in less than 10% of all experiments (Supplementary Table 3), which could be missed using other connectivity mapping techniques. Clustered inputs are found in NDB (fraction of whole brain inputs in NDB > 0 in 93% of all experiments) and substantia innominata (SI) (fraction of whole brain inputs in SI > 0 in 75% of all experiments) for putative cholinergic neurons, in LC (fraction of whole brain inputs in LC > 0 in 66% of all experiments) for putative noradrenergic neurons, and in DR (~0.01% of whole brain inputs, found in 63% of all experiments) for putative serotonergic neurons. The numbers of independent experiments with similar results are 121 in a, 61 in a’, 52 in a’, 254 in b, 165 in b’, 137 in b’, 278 in c, 187 in c’, 149 in c’, 236 in d, 187 in d’, 68 in d’, 226 in e, 110 in e’, 152 in e’, 275 in f, 224 in f’, 198 in f’, 214 in g, 187 in g’, 33 in g’, 231 in h, 193 in h’, 193 in h’, 53 in i, 52 in i’, and 30 in i’. Enlarged views of boxed areas are shown in the right-hand panels for each major brain structure. Arrows highlight the location of single labeled cells.