Version history

{
  "kind": "infographic",
  "prompt": "Three generations of mouse-cortex methods (paired patch, small-EM, MICrONS dense EM) independently converge on a like-to-like wiring rule among V1 excitatory pyramidal cells, with the rule expressed through synapse number/density, EPSP amplitude, and network modularity.",
  "provider": "other",
  "raw_fields": {
    "papers": [
      {
        "n": 94,
        "doi": "10.1038/nature09880",
        "value": "Cochran–Armitage trend p = 0.040",
        "method": "paired patch-clamp",
        "metric": "P(connection) trend with ΔOri",
        "n_analyzed": "94",
        "ci_or_error": "p = 0.040",
        "text_access": "fulltext",
        "n_definition": "orientation-selective potential pairs",
        "scope_region": "mouse V1 L2/3",
        "study_system": "Mouse V1 L2/3 pyramidal cells",
        "taxonomic_level": "broad excitatory subclass",
        "scope_population": "orientation-selective pairs",
        "value_source_sentence": "Connectivity rate decreased with increasing difference in orientation preference (P = 0.040, Cochran-Armitage test for trend,).",
        "experimental_conditions": "in vitro paired patch + in vivo 2P"
      },
      {
        "n": 26,
        "doi": "10.1038/nature14182",
        "value": "1.38 mV vs 0.12 mV",
        "method": "paired patch-clamp",
        "metric": "Median EPSP amplitude (correlated > 0.2 vs < 0)",
        "n_analyzed": "26",
        "ci_or_error": "Wilcoxon p = 6.8 × 10⁻⁵",
        "text_access": "fulltext",
        "n_definition": "connected pairs partitioned by response correlation",
        "scope_region": "mouse V1 L2/3",
        "study_system": "Mouse V1 L2/3 pyramidal cells",
        "taxonomic_level": "broad excitatory subclass",
        "scope_population": "connected pyramidal pairs",
        "value_source_sentence": "Importantly, response correlation was closely related to EPSP amplitude: the strongest connections were found between neuronal pairs with the highest response correlations (;), while neurons with negatively correlated responses tended not to connect or formed only weak connections (response correlation > 0.2, median amplitude of connected pairs: 1.38 mV,= 10; response correlation < 0, median amplitude: 0.12 mV,= 16;= 6.8 × 10, Wilcoxon rank-sum test;).",
        "experimental_conditions": "in vitro paired patch + in vivo 2P"
      },
      {
        "n": 201,
        "doi": "10.1038/nature17192",
        "value": "0.55 ± .003 vs 0.50 ± .009 null",
        "method": "EM connectomic",
        "metric": "Network modularity (preferred-orientation grouping)",
        "n_analyzed": "201",
        "ci_or_error": "permutation p ≈ 0",
        "text_access": "fulltext",
        "n_definition": "connected-core neurons (degree ≥ 2)",
        "scope_region": "mouse V1 L2/3",
        "study_system": "Mouse V1 L2/3 EM reconstruction",
        "taxonomic_level": "broad excitatory subclass",
        "scope_population": "EM-reconstructed pyramidal network",
        "value_source_sentence": "Modularity in the reconstructed network was significantly higher than would be expected by chance (= 0.55 ± .003 vs. 0.50 ± .009, mean ± SD,≈ 0, Permutation test;and, see Methods) and was not a consequence of higher order motifs ().",
        "experimental_conditions": "EM + in vivo 2P"
      },
      {
        "n": 1,
        "doi": "10.1038/s41586-025-08840-3",
        "value": "Graded positive association",
        "method": "EM connectomic + digital-twin features",
        "metric": "Functional similarity vs synaptic density",
        "n_analyzed": "1",
        "ci_or_error": null,
        "text_access": "fulltext",
        "n_definition": "all ADP-controlled pairs in MICrONS proofread subset",
        "scope_region": "mouse VISp + HVAs",
        "study_system": "Mouse VISp + AL/LM/RL",
        "taxonomic_level": "broad excitatory subclass",
        "scope_population": "all functionally responsive proofread cells",
        "value_source_sentence": "Specifically, higher-than-average rates of synaptic density (synapses per unit) were associated with higher-than-average functional similarity, again in a graded fashion.",
        "experimental_conditions": "EM dense reconstruction + digital twin features"
      }
    ],
    "audit_issues": [
      {
        "dimension": "metric_definition",
        "description": "Statistics are different across rows: ΔOri trend p-value (Ko 2011), median EPSP amplitude by response correlation (Cossell 2015), network modularity Q (Lee 2016), functional-similarity vs. synaptic-density gradient (MICrONS). Cannot be plotted on a single scalar axis.",
        "entries_affected": [
          "10.1038/nature09880",
          "10.1038/nature14182",
          "10.1038/nature17192",
          "10.1038/s41586-025-08840-3"
        ]
      },
      {
        "dimension": "scope_region",
        "description": "MICrONS spans V1 + 3 higher visual areas across layers; the older studies are V1 L2/3-only.",
        "entries_affected": [
          "10.1038/s41586-025-08840-3"
        ]
      }
    ],
    "audit_verdict": "CAVEAT",
    "comparison_id": "like-to-like-mouse-V1-E-to-E",
    "comparison_name": "Like-to-like excitatory connection rule across mouse V1 paired-recording and EM studies",
    "comparison_type": "convergent evidence",
    "what_it_reveals": "Three generations of mouse-cortex methods (paired patch, small-EM, MICrONS dense EM) independently converge on a like-to-like wiring rule among V1 excitatory pyramidal cells, with the rule expressed through synapse number/density, EPSP amplitude, and network modularity.",
    "homogeneity_check": {
      "caveats": [
        "MICrONS (08840-3) spans V1 + 3 higher visual areas, whereas the older studies are V1-only.",
        "Metrics differ: ΔOri trend (09880), EPSP amplitude (14182), network modularity (17192), feature-similarity gradient (08840-3) — all probe the same underlying rule but cannot be directly averaged."
      ],
      "n_definition_uniform": "false",
      "scope_region_uniform": "false",
      "taxonomic_level_uniform": "true",
      "scope_population_uniform": "false"
    },
    "suggested_plot_type": "forest plot",
    "mandatory_caption_caveats": [
      "Four different statistics (trend p, EPSP by correlation, modularity Q, similarity-density gradient) probe the same like-to-like rule and are not directly averageable.",
      "MICrONS row covers V1 + higher visual areas including feedback; the older rows are V1 L2/3 only."
    ]
  },
  "section_id": "section_06",
  "source_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence/blob/79ce062d54a924ce05953ec90aa9d26044d2b48f/evidence/section_06_evidence_package.json",
  "target_ref": "wiki_page:computationalreviewrecurrence-06-connectomic-micons",
  "review_repo": "ComputationalReviewRecurrence",
  "section_ref": "wiki_page:computationalreviewrecurrence-06-connectomic-micons",
  "source_path": "evidence/section_06_evidence_package.json",
  "source_refs": [
    "paper:paper-31c9e0b4d258",
    "paper:paper-7ac22819c082",
    "paper:paper-c4ad527c9bfb",
    "paper:paper-d2a8c6775359"
  ],
  "section_title": "6. Connectomic resolution — MICrONS mouse V1/HVA millimetre-scale EM volume; pyramidal-pyramidal wiring statistics derived from it; reconciliation with paired-recording estimates",
  "source_policy": {
    "mode": "public_source_pointer_with_short_context",
    "notes": [
      "Local review repositories are read-only inputs.",
      "SciDEX stores paper metadata, structured evidence, file pointers, and short citation contexts; it does not copy full review prose."
    ],
    "source_commit_sha": "79ce062d54a924ce05953ec90aa9d26044d2b48f",
    "source_repository_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence"
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  "generation_status": "complete",
  "review_bundle_ref": "analysis_bundle:ab-d9c479db9be9",
  "origin_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence/blob/79ce062d54a924ce05953ec90aa9d26044d2b48f/evidence/section_06_evidence_package.json",
  "commit_sha": "79ce062d54a924ce05953ec90aa9d26044d2b48f",
  "created_by": "persona-jerome-lecoq-gbo-neuroscience",
  "repository_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence"
}