Fig. 5: Connectivity analysis enabled by NEURD.

a, Schematic illustrating two proximities between a pair of neurons (axon passing within 5 μm radius of a dendrite). Only one proximity has a synapse, thus the ‘conversion rate’ is 50%. b, Cumulative density function (CDF) of the postsynaptic dendritic skeletal walks for different connection types, demonstrating that excitatory inputs occur further along the dendrite from the soma (see Supplementary Fig. 23 for more details). c, Mean conversion rate as a function of distance along the axon (see Supplementary Fig. 23 for more details). d,e, Conversion rates (synapses/proximities) for different excitatory and inhibitory combinations. The x-axis represents the maximum distance that is considered a proximity. f, Conversion rates for different cell-type subclasses and compartments are largely consistent with previous studies (MICrONS; cell-type labels generated from a GNN classifier; see Supplementary Table 1 for glossary and Supplementary Fig. 24 for more conversion rates). g, The frequency (mean ± s.d.) of reciprocal connections or edge-dense three-node motifs was enriched compared with null distributions where synaptic degree distribution is held the same but edges are shuffled (orange), where the synaptic edges are shuffled across existing proximity edges (green) or where synapses are randomly shuffled (red); 250 random graph samples for each null distribution comparison (see Supplementary Fig. 25 for more details and inhibitory/excitatory-only graphs). h, Example multi-synaptic connection (n = 7 synapses) from an excitatory to inhibitory neuron (H01). i, Distribution of response correlation mean (±s.e.m.) between pairs of functionally matched excitatory neurons (MICrONS). Response correlation is significantly larger for pairs of neurons with 4 or more synapses connecting them (n = 11 pairs) compared with those with 1, 2 or 3 synapses (n = 5,350, 280 or 34 pairs, respectively; see Supplementary Fig. 27 for more details). See Supplementary Table 2 for all associated n values.