Version history

{
  "kind": "infographic",
  "prompt": "Mouse-cortex EM volume size has grown roughly 300-fold from Bock 2011 (~0.008 mm³) to MICrONS 2025 (~1 mm³), with corresponding growth in reconstructed neuron and synapse counts.",
  "provider": "other",
  "raw_fields": {
    "papers": [
      {
        "n": 1500,
        "doi": "10.1038/nature09802",
        "value": "450 × 350 × 52 μm",
        "method": "ssTEM",
        "metric": "EM volume",
        "n_analyzed": "1500",
        "ci_or_error": null,
        "text_access": "fulltext",
        "n_definition": "cell bodies in EM volume",
        "scope_region": "mouse V1",
        "study_system": "Mouse V1 L1/2/3/upper-4",
        "taxonomic_level": "broad mixed-cell-type volume",
        "scope_population": "L1-upper L4",
        "value_source_sentence": "The raw image data was approximately 36 terabytes (TB), with the final stitched and registered EM data set encompassing approximately ten million megapixels (10 TB), spanning ~450 x 350 x 52 μm and containing approximately 1500 cell bodies ().",
        "experimental_conditions": "TEMCA, 4 × 4 × 50 nm voxels"
      },
      {
        "n": 1278,
        "doi": "10.1038/nature17192",
        "value": "450 × 450 × 150 μm",
        "method": "ssTEM",
        "metric": "EM volume",
        "n_analyzed": "1278",
        "ci_or_error": null,
        "text_access": "fulltext",
        "n_definition": "reconstructed neuronal targets",
        "scope_region": "mouse V1",
        "study_system": "Mouse V1 L2/3",
        "taxonomic_level": "broad mixed-cell-type volume",
        "scope_population": "L2/3 pyramidal cells + targets",
        "value_source_sentence": "3700 serial sections (< 50 nm thick) were cut and imaged spanning a 450 × 450 × 150 μm volume at 4 × 4 × 40 nm/voxel resolution.",
        "experimental_conditions": "TEMCA, 4 × 4 × 40 nm voxels"
      },
      {
        "n": 500,
        "doi": "10.1038/s41467-020-18659-3",
        "value": "~0.003 mm³ (≈500 neurons)",
        "method": "ssTEM (autoTEM)",
        "metric": "Pilot EM volume",
        "n_analyzed": "500",
        "ci_or_error": null,
        "text_access": "fulltext",
        "n_definition": "neurons in pilot autoTEM volume",
        "scope_region": "mouse V1",
        "study_system": "Mouse V1 L2/3",
        "taxonomic_level": "broad mixed-cell-type volume",
        "scope_population": "L2/3",
        "value_source_sentence": "The pilot dataset contained about 500 neurons and 3.2 million synapses, spanning over layer 2/3 mouse primary visual cortex, which have been analyzed to examine network connectivity of pyramidal and chandelier cells.",
        "experimental_conditions": "autoTEM pipeline"
      },
      {
        "n": 144120,
        "doi": "10.1038/s41586-025-08790-w",
        "value": "1.3 × 0.87 × 0.82 mm (≈1 mm³)",
        "method": "ssTEM",
        "metric": "EM volume",
        "n_analyzed": "94010",
        "ci_or_error": null,
        "text_access": "fulltext",
        "n_definition": "automatically segmented nuclei (subvolume 65); 94,010 high-quality detections from perisomatic features paper",
        "scope_region": "mouse VISp + HVAs",
        "study_system": "Mouse VISp + AL + LM + RL",
        "taxonomic_level": "broad mixed-cell-type volume",
        "scope_population": "all cells across layers 1–6",
        "value_source_sentence": "Here we present a dataset (Fig.) that bridges neuronal function and connectivity at the cubic millimetre scale in mouse visual cortex (in vivo dimensions 1.3 × 0.87 × 0.82 mm).",
        "experimental_conditions": "autoTEM pipeline, two subvolumes, dense reconstruction"
      }
    ],
    "audit_issues": [
      {
        "dimension": "sample_size",
        "description": "n_definition varies (reconstructed targets vs. neurons in pilot vs. automatically segmented nuclei in subvolume vs. perisomatic-features detections). Volumes are commensurable but neuron counts use different denominators.",
        "entries_affected": [
          "10.1038/nature09802",
          "10.1038/nature17192",
          "10.1038/s41467-020-18659-3",
          "10.1038/s41586-025-08790-w"
        ]
      }
    ],
    "audit_verdict": "CAVEAT",
    "comparison_id": "mouse-cortex-EM-volume-scale",
    "comparison_name": "Mouse cortex EM volume size across studies",
    "comparison_type": "timeline",
    "what_it_reveals": "Mouse-cortex EM volume size has grown roughly 300-fold from Bock 2011 (~0.008 mm³) to MICrONS 2025 (~1 mm³), with corresponding growth in reconstructed neuron and synapse counts.",
    "homogeneity_check": {
      "caveats": [
        "n_definition varies across papers (reconstructed targets, neurons in pilot, nuclei detections); raw volume dimensions are comparable but cell-population counts use different denominators."
      ],
      "n_definition_uniform": "false",
      "scope_region_uniform": "true",
      "taxonomic_level_uniform": "true",
      "scope_population_uniform": "true"
    },
    "suggested_plot_type": "timeline",
    "mandatory_caption_caveats": [
      "Raw EM volumes are commensurable, but reported cell counts use different denominators (reconstructed neurons, pilot-only counts, automatically segmented nuclei). State the denominator for any neuron-count axis."
    ]
  },
  "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-38c4084b5c1d",
    "paper:paper-a80aa5d68f45",
    "paper:paper-aecac0566e4a",
    "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"
}