In the V1 Deep Dive mouse, connected excitatory neurons had only slightly more similar movie responses than nearby unconnected neurons; the same test gave a 2 to 7 times larger effect in MICrONS
Question: the MICrONS study (Ding et al. 2025) found that connected excitatory neurons in mouse visual cortex respond more similarly to natural movies than unconnected neurons with the same axon-dendrite proximity. Does this like-to-like rule have the same size in a second mouse? Approach: we used the Allen V1 Deep Dive (V1DD) dataset (EM materialization 1196 and two-photon imaging of the same tissue, CC BY 4.0). 553 neurons are manually coregistered; 193 have proofread axons; they make 1,441 connections onto coregistered neurons with function and proximity. Proximity came from synapse-site clouds: axon output sites within 10 um of the input sites of the target. We compared each connected pair with unconnected pairs of the same presynaptic cell, proximity decile, session and lateral distance bin, in standard-deviation (SD) units. We applied the same code to the MICrONS functional connectomics release. Results: in MICrONS (V1 to V1, in vivo movie signal correlation, 2,840 connections) the effect was 0.147 SD (95% CI 0.103-0.183), and 0.180 SD for L2/3 and L4 presynaptic cells. In V1DD it was 0.022 SD (-0.021-0.066) with deconvolved events and 0.053 SD (0.007-0.101) with dF/F; for L2/3 and L4 presynaptic cells 0.057 and 0.092 SD; L5 presynaptic cells showed none. The V1DD effect was 15-51% of the MICrONS effect (bootstrap p = 0.0005-0.022). Our proximity proxy gave an equal or larger MICrONS effect (0.159 SD) than skeleton co-travel, response reliability was equal (median CC_max 0.64 in both), and MICrONS samples of the V1DD size detected the effect 200 of 200 times. Gratings, natural images, sparse-noise maps and orientation preference also gave effects below 0.06 SD in V1DD. Connected same-session V1DD pairs had slightly higher movie noise correlations (0.07 SD, p = 0.025). Multi-synapse pairs were more similar than single-synapse pairs in both mice. Main limitations: V1DD coregistration errors cannot be measured; stimuli (one 120 s movie versus six 10 s clips) and sampled depths differ; two animals cannot give the distribution across mice. Conclusion: the rule replicates in direction for L2/3 and L4 presynaptic neurons, but the single-animal MICrONS effect size is not general.
functional connectomics · like-to-like connectivity · V1 Deep Dive · V1DD · MICrONS · mouse visual cortex · electron microscopy · two-photon imaging · signal correlation · replication · axon-dendrite proximity · coregistration
References
7- usesdoi:10.1038/s41586-025-08840-3
We use the Ding et al. 2025 MICrONS functional connectomics release (node and edge tables) as the reference, and we test whether its like-to-like effect size repeats in a second mouse. The direction repeats; the size is 2 to 7 times smaller in V1DD.
- usesdoi:10.1038/s41586-025-08790-w
We use the MICrONS minnie65 v1507 synapse table to compute our synapse-site proximity proxy in MICrONS.
- In MICrONS mouse visual cortex, connected excitatory neurons had more similar preferred orientations mainly when their synapses were large (14,412 neurons, digital-twin tuning) sci:sha256:07b8a9b83eea2b7443dc99d29805440aefc0d23414bb9c8959decc534824bd92
Earlier SCI study of orientation like-to-like wiring and synapse size in MICrONS only; our study adds a second mouse.
- Excitatory axons, but not basket cell axons, selected excitatory targets with similar orientation beyond axon–dendrite overlap and 10 µm soma distance in MICrONS mouse visual cortex sci:sha256:3475d3289a96669e6e83d55e0fc9ec509894213422121532387c543739c8dca2
Earlier SCI study of excitatory and basket-cell output specificity in MICrONS only.
- usesdoi:10.3389/fncom.2016.00010
We use the CC_max reliability measure of Schoppe et al. 2016, as MICrONS did.
- doi:10.1038/nature09880
First report of like-to-like connectivity in mouse V1 with paired recordings.
- doi:10.7554/eLife.38173
CaImAn spike inference, used for the MICrONS in vivo responses.
Cited by
11 publicationsPublic catalog entries on Sciscape.
- usesRecorded movie similarity gave no clear loss decrease after model similarity in a fixed test of 234,393 MICrONS pairs from one mouse
We reuse its cached publisher files and build on its comparison of empirical function and anatomy. We independently check the files against the publisher. We do not reuse its analysis code.
- Population coupling predicted input connections in two mouse V1 EM volumes as in slices (odds ratio 1.25–1.36 per SD), but within layer 2/3 of MICrONS the ratio was only 1.03–1.09
Earlier structure-function test on the same matched V1DD and MICrONS cohorts (response similarity of connected cells).
- In one mouse visual cortex volume, like-to-like synapses formed on basal and apical dendrites in proportion to axon–dendrite contact, for within-area, feedforward and feedback axons
Re-test of the Ding et al. like-to-like rule in a second mouse; source of the edge-table checksums we matched.
- usesIn one mouse V1 panel, a half-second lag score agreed with 142 of 310 recorded one-way synapse directions
This source supplies the original matched V1 Deep Dive cohort and functional session and ROI choices. Its complete signed package was verified.
- usesIn one V1DD mouse, mean synapse size had no clear relation to movie response similarity in 1,441 connections after cell, count and geometry controls
We use its verified V1DD response and anatomy tables. We add a mean synapse size test with source and target cell controls.
- Measured movie similarity gave no clear added wiring gain over model similarity with test neurons excluded in one MICrONS mouse
This prior test compares measured like-to-like effects in two mice and identifies the same MICrONS response release.
- usesWith bounded spline models, mean cleft size gave no clear added prediction gain for movie response similarity in two mouse V1 samples
We use four verified supporting data extracts from its V1 Deep Dive analysis. We rebuild mean cleft size from count and total size and audit those values against its synapse records.
- Recorded synapses gave a 0.025% error decrease beyond a digital twin in a calibration test of 91,647 MICrONS V1 pairs
Prior SCI work compares connection presence and measured response similarity in V1DD and MICrONS. Our task tests added prediction after digital twin correlation is given.
- usesVariation within movie repeats supplied 83% of the fitted common input slope in one mouse V1 calcium panel
This is the upstream source of the matched V1DD cohort and original functional summaries, supplied through the cited Shared Input Study.
- usesRemoving connections with no size slope information reduced an HC1 variance estimate by 53% and 9% in two mouse cortex models
This study supplies the verified V1DD functional and individual-synapse tables. We checked the selected counts and size sums.
- usesIn one V1DD mouse, shared inputs from imaged cells had no clear link to movie noise correlation in 6,416 pairs after controls
We reuse its verified V1DD cell, synapse, and response tables. Its code defines the functional measurements. We rebuilt the movie measures from public traces.