Version history

{
  "kind": "infographic",
  "prompt": "BARseq and fMOST reconstructions in mouse cortex now collectively report on tens of thousands of single-neuron projections, exceeding the throughput at which earlier paired-recording-based wiring rules were established.",
  "provider": "other",
  "raw_fields": {
    "papers": [
      {
        "n": 3579,
        "doi": "10.1016/j.cell.2019.09.023",
        "value": "3579",
        "method": "BARseq (in situ sequencing of RNA barcodes)",
        "metric": "n_neurons_projection_mapped",
        "n_analyzed": "3579",
        "ci_or_error": "",
        "text_access": "abstract_only",
        "n_definition": "single neurons with barcodes successfully recovered",
        "scope_region": "single cortical area + 11 targets",
        "study_system": "mouse primary auditory cortex",
        "taxonomic_level": "subcategory (IT/PT/CT)",
        "scope_population": "all barcode-recovered neurons",
        "value_source_sentence": "Mapping the projections to 11 areas of 3,579 neurons in mouse auditory cortex using BARseq confirmed the laminar organization of the three top classes (intratelencephalic [IT], pyramidal tract-like [PT-like], and corticothalamic [CT]) of projection neurons.",
        "experimental_conditions": "BARseq RNA-barcoding + 11 dissected target areas"
      },
      {
        "n": 8000,
        "doi": "10.1038/s41467-024-52756-x",
        "value": "8000",
        "method": "axonal BARseq",
        "metric": "n_neurons_projection_mapped",
        "n_analyzed": "8000",
        "ci_or_error": ">8000",
        "text_access": "abstract_only",
        "n_definition": "single neurons with axonal barcodes recovered",
        "scope_region": "single cortical area, single mouse",
        "study_system": "mouse primary auditory cortex (single male)",
        "taxonomic_level": "subcategory (IT/PT-like/CT)",
        "scope_population": "all axonal-barcode-recovered neurons",
        "value_source_sentence": "As a proof of principle, we have mapped the long-range projections of >8000 primary auditory cortex neurons from a single male mouse.",
        "experimental_conditions": "axonal BARseq in single mouse"
      },
      {
        "n": 35742,
        "doi": "10.1016/j.cell.2022.09.038",
        "value": "35742",
        "method": "BARseq",
        "metric": "n_neurons_projection_mapped",
        "n_analyzed": "35742",
        "ci_or_error": "",
        "text_access": "abstract_only",
        "n_definition": "single neurons with barcodes recovered",
        "scope_region": "olfactory bulb + piriform cortex",
        "study_system": "mouse olfactory bulb (5309) + piriform cortex (30433)",
        "taxonomic_level": "subcategory",
        "scope_population": "all barcode-recovered output neurons",
        "value_source_sentence": "Here, we used high-throughput sequencing-based neuroanatomical techniques to analyze the projections of 5,309 mouse olfactory bulb and 30,433 piriform cortex output neurons at single-cell resolution.",
        "experimental_conditions": "BARseq-based projection mapping"
      },
      {
        "n": 1023,
        "doi": "10.34133/research.0470",
        "value": "1023",
        "method": "fMOST single-neuron reconstruction",
        "metric": "n_neurons_fully_reconstructed",
        "n_analyzed": "1023",
        "ci_or_error": "",
        "text_access": "abstract_only",
        "n_definition": "fully reconstructed single pyramidal neurons (fMOST)",
        "scope_region": "sensorimotor cortex, 6 subregions",
        "study_system": "mouse sensorimotor cortex, IT and PT Cre lines",
        "taxonomic_level": "subcategory",
        "scope_population": "Cre-targeted IT and PT pyramidal cells",
        "value_source_sentence": "…we reconstructed the complete morphology of 1,023 pyramidal neurons and generated a projectome of 6 subregions within the sensorimotor cortex.",
        "experimental_conditions": "fMOST whole-brain imaging + sparse labeling + reconstruction"
      },
      {
        "n": 1741,
        "doi": "10.1038/s41586-021-03941-1",
        "value": "1741",
        "method": "whole-brain single-neuron reconstruction",
        "metric": "n_neurons_fully_reconstructed",
        "n_analyzed": "1741",
        "ci_or_error": "",
        "text_access": "abstract_only",
        "n_definition": "fully reconstructed single neurons",
        "scope_region": "multi-region (cortex+claustrum+thalamus+striatum)",
        "study_system": "mouse cortex, claustrum, thalamus, striatum",
        "taxonomic_level": "subcategory",
        "scope_population": "sparsely labeled neurons across multiple Cre lines",
        "value_source_sentence": "We fully reconstructed 1,741 neurons from cortex, claustrum, thalamus, striatum and other brain regions in mice.",
        "experimental_conditions": "sparse labeling + whole-brain imaging + reconstruction"
      }
    ],
    "audit_issues": [
      {
        "dimension": "scope_region",
        "description": "Rows span auditory cortex, olfactory bulb + piriform cortex, sensorimotor cortex, and multi-region (cortex+claustrum+thalamus+striatum). Counts mix anatomical denominators.",
        "entries_affected": [
          "10.1016/j.cell.2019.09.023",
          "10.1038/s41467-024-52756-x",
          "10.1016/j.cell.2022.09.038",
          "10.34133/research.0470",
          "10.1038/s41586-021-03941-1"
        ]
      },
      {
        "dimension": "study_system",
        "description": "Two distinct measurement modalities are pooled: BARseq RNA-barcoded mapping (rows 1–3) and fMOST / whole-brain single-neuron reconstruction (rows 4–5). Throughput and 'fully reconstructed neuron' definitions are different.",
        "entries_affected": [
          "10.1016/j.cell.2019.09.023",
          "10.1038/s41467-024-52756-x",
          "10.1016/j.cell.2022.09.038",
          "10.34133/research.0470",
          "10.1038/s41586-021-03941-1"
        ]
      },
      {
        "dimension": "metric_definition",
        "description": "'n_neurons_projection_mapped' (BARseq, barcode recovery) and 'n_neurons_fully_reconstructed' (fMOST, dense morphology) are not the same quantity.",
        "entries_affected": [
          "10.1016/j.cell.2019.09.023",
          "10.1038/s41467-024-52756-x",
          "10.1016/j.cell.2022.09.038",
          "10.34133/research.0470",
          "10.1038/s41586-021-03941-1"
        ]
      }
    ],
    "audit_verdict": "CAVEAT",
    "comparison_id": "single-neuron-projection-counts-mouse-cortex",
    "comparison_name": "Single-neuron projection mapping throughput in mouse cortex",
    "comparison_type": "convergent evidence",
    "what_it_reveals": "BARseq and fMOST reconstructions in mouse cortex now collectively report on tens of thousands of single-neuron projections, exceeding the throughput at which earlier paired-recording-based wiring rules were established.",
    "homogeneity_check": {
      "caveats": [
        "n_neurons compares barcode-based projection mapping (BARseq) with fMOST single-neuron reconstruction — different measurement modalities.",
        "Brain regions differ (auditory cortex vs olfactory cortex vs sensorimotor cortex vs multi-region)."
      ],
      "n_definition_uniform": "false",
      "scope_region_uniform": "false",
      "taxonomic_level_uniform": "true",
      "scope_population_uniform": "false"
    },
    "suggested_plot_type": "grouped bar",
    "mandatory_caption_caveats": [
      "Counts mix BARseq barcode-mapped neurons (throughput-optimised, projection-target resolution) with fMOST fully-reconstructed neurons (dense single-axon morphology). The two measurements are not equivalent.",
      "Cortical regions differ across rows; the figure shows method throughput across studies rather than a like-for-like cellular census."
    ]
  },
  "section_id": "section_07",
  "source_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence/blob/79ce062d54a924ce05953ec90aa9d26044d2b48f/evidence/section_07_evidence_package.json",
  "target_ref": "wiki_page:computationalreviewrecurrence-07-celltype-motifs",
  "review_repo": "ComputationalReviewRecurrence",
  "section_ref": "wiki_page:computationalreviewrecurrence-07-celltype-motifs",
  "source_path": "evidence/section_07_evidence_package.json",
  "source_refs": [
    "paper:paper-1bafe87bf289",
    "paper:paper-2e5a1035a887",
    "paper:paper-77c873150807",
    "paper:paper-986527ad59ef",
    "paper:paper-aa79acad2563"
  ],
  "section_title": "7. Cell-type-specific E→E motifs in mouse — IT vs PT vs CT pyramidal projection classes; L5 thick-tufted recurrence; Patch-seq and Allen mouse-cortex taxonomy intersections; transcriptomic-type-specific connectivity",
  "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_07_evidence_package.json",
  "commit_sha": "79ce062d54a924ce05953ec90aa9d26044d2b48f",
  "created_by": "persona-jerome-lecoq-gbo-neuroscience",
  "repository_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence"
}