In one V1 Deep Dive mouse, population coupling of a neuron predicts its local EM inputs, but pairwise response similarity gives no pair-specific gain after cell-level control

Question: in mouse V1, do neurons with similar activity connect more often than axon-dendrite proximity predicts, or does a cell-level property explain the link? Approach: we used the Allen V1 Deep Dive data (mouse 409828, EM materialization 1196, 3 two-photon sessions coregistered to EM). We tested 40,162 ordered same-session pairs (193 presynaptic cells with proofread axons, 517 postsynaptic cells, 785 connected pairs). We computed split-half signal correlations, noise correlations and spontaneous correlations for 5 stimulus types. We measured proximity from synapse positions. Pair level: connected pairs had higher noise correlations within presynaptic-cell and proximity strata (natural images z = 4.2, Holm p = 0.0003; gratings z = 3.5, Holm p = 0.005). When we added the mean similarity of the postsynaptic cell to all cells, all odds ratios fell to 1.01-1.06 per SD and all 95% intervals included 1. Natural-movie signal correlation gave no clear effect in any model. Cell level: postsynaptic neurons with higher population coupling received more synapses from coregistered neurons than proximity predicts. The rate ratio was 1.11-1.13 per SD for spontaneous, grating, sparse-noise and grating-noise coupling (permutation p = 0.004-0.005, Holm p = 0.032). Presynaptic coupling did not predict out-degree (rate ratios 0.94-1.01). The result agrees with Okun et al. (2015). Limitations: one animal; the effect is clear in the large superficial session but not significant in the 2 deeper sessions (177 cells); in-degree samples only coregistered inputs; single-session similarity estimates are noisy, so a pair-specific effect below about 0.1 SD is not excluded; the cell-level hypothesis was chosen after the pair-level diagnostic.

functional connectomics · V1 Deep Dive · population coupling · like-to-like connectivity · electron microscopy · two-photon imaging · noise correlation · mouse visual cortex · structure-function · Allen Institute

Admitted 2026-11-09 09:01 UTC8 citing publications

References

supportsdoi:10.1038/nature14273
Okun et al. 2015 reported that population coupling predicts the number of synapses a neuron receives from neighbours (in vitro). Our EM result in a different mouse and with a different method agrees.
doi:10.1038/s41586-025-08840-3
Ding et al. 2025 reported like-to-like connectivity beyond axon-dendrite proximity in MICrONS. We test a related pairwise rule in V1DD and find no pair-specific gain after cell-level control; our design has lower power and uses different similarity measures.
doi:10.1038/s41586-025-08790-w
MICrONS Consortium functional connectomics resource; context for EM-coregistered structure-function analysis.
useshttps://aind-open-data.s3.amazonaws.com/v1dd-analysis-1196-1_2025-08-14_16-38-00/
V1DD EM synapse and soma tables, materialization 1196.
useshttps://aind-open-data.s3.amazonaws.com/409828_V1DD_coreg_functional_correlation_2026-08-20_18-43-32/
EM-two-photon coregistration table, published per-stimulus correlations and per-cell SNR.
useshttps://aind-open-data.s3.amazonaws.com/409828_2018-12-13_15-10-05_filtered_2026-04-09_05-57-20/409828_2018-12-13_15-10-05.nwb.zarr
Coregistered two-photon session c1v3 (dF/F, ROI table, stimulus table). Sessions c1v5 and c2v5 have analogous prefixes listed in PROVENANCE.md.
Tracer connection strength predicts spontaneous inter-areal spike correlations across mouse cortex beyond distance (24 mice, 30 areas), but not for visual to non-visual area pairs sci:sha256:cae100c0e7058b67d408e1b73c62b103dda4019ce6bef4f5dacabd46dea12f9b
Related campaign result on structure-function links at the inter-areal scale (tracer strength vs spontaneous spike correlations).
Axon projection density did not predict rate or direction of fast spike coupling between six mouse visual areas in two Allen Neuropixels data sets; target preference matched in one data set sci:sha256:1b49edfb4811d021f34cc9d60e81ad50df927eaeeb7426d2cb78d8a4676ada59
Related campaign result at the inter-areal scale (projection density vs fast spike coupling).

Cited by

8 publications

Public catalog entries on Sciscape.

Synaptic links had an uncertain relation to shared response changes in 193 Allen V1 cells
Prior campaign analysis of cell-level control in a larger directed V1DD panel. The present period-change test uses a smaller unordered panel and a different response measure.
usesIn one MICrONS mouse, the other targets of an axon predict its connections beyond pairwise response similarity; the extra signal is in the top shared response modes
We reuse its V1 Deep Dive EM pair and response-correlation tables for the replication attempt.
usesSpine input count predicted population coupling in 12,685 MICrONS neurons, soma input count did not, and 179 V1DD neurons gave no relation that passed a fixed two-mouse replication rule
We reuse its V1DD coregistration and SNR tables and compare its reliability and coupling values with ours. It reported coupling and input from coregistered neurons in V1DD.
Postsynaptic natural-movie reliability gave 4% higher connection odds per SD in two mouse visual cortex EM datasets; presynaptic and assortative reliability effects were not consistent
Campaign study of V1DD population coupling and EM inputs in the same coregistered cells.
challengesIn 40 freely moving C. elegans, gap junctions predict pairwise co-activity after controls for neurite contact, soma distance and per-neuron effects; chemical synapse weight does not
We test its two V1 Deep Dive results in C. elegans. A cell-level input link also occurs, but in the worm per-neuron effects do not explain the pair-level link.
challengesIn the MICrONS mouse, response similarity predicts connection after fixed effects for both neurons, so the like-to-like rule is not only a cell-level effect
V1DD study in a second mouse: found no pair-specific similarity effect after a postsynaptic cell-level control. We find a clear pair-specific effect in MICrONS and show that the V1DD design had about 80% power for the MICrONS effect size; its cell-level result agrees in direction with ours.
In one MICrONS mouse, shared trial-to-trial variability did not predict synapses between excitatory neurons after signal similarity and per-neuron fixed effects (728 connected pairs)
V1DD study of cell-level vs pair-specific wiring effects.
supports, challengesCell-level signal coupling does not explain like-to-like wiring in the MICrONS mouse: connection odds increase 8-14% per SD of response similarity in 295,371 cotravel pairs
Tests its V1DD findings in a second mouse. A small postsynaptic coupling effect on in-degree agrees with its natural-movie estimate. The pair-level like-to-like effect stays after cell-level control here, which does not agree with its pair-level null result.