Version history

{
  "scope": "Adult mouse whole brain (MERFISH + scRNA-seq atlas, BICCN-affiliated)",
  "claim_text": "A MERFISH atlas of more than 1,100 genes in approximately 10 million cells across the entire adult mouse brain yielded a comprehensive >5,000-cluster cell-type taxonomy in >300 major classes — setting the spatial-transcriptomic baseline against which mouse-cortex E→E circuit cell-type claims must now be matched.",
  "raw_fields": {
    "n": 10000000,
    "doi": "10.1038/s41586-023-06808-9",
    "claim": "A MERFISH atlas of more than 1,100 genes in approximately 10 million cells across the entire adult mouse brain yielded a comprehensive >5,000-cluster cell-type taxonomy in >300 major classes — setting the spatial-transcriptomic baseline against which mouse-cortex E→E circuit cell-type claims must now be matched.",
    "cite_key": "Zhang2023b",
    "evidence": "MERFISH + scRNA-seq integration; >10 million cells; >5,000 clusters in >300 major cell types; CCF-registered.",
    "effect_size": ">10 million cells; >5,000 clusters; >300 major cell types",
    "text_access": "fulltext",
    "study_system": "Adult mouse whole brain (MERFISH + scRNA-seq atlas, BICCN-affiliated)",
    "argument_role": "supporting",
    "replication_status": "paired-with-Yao2023",
    "claim_source_sentence": "Here we imaged a panel of more than 1,100 genes in approximately 10 million cells across the entire adult mouse brains using multiplexed error-robust fluorescence in situ hybridization12 and performed spatially resolved, single-cell expression profiling at the whole-transcriptome scale by integrating multiplexed error-robust fluorescence in situ hybridization and single-cell RNA sequencing data.",
    "source_provenance_status": "ok",
    "replication_evidence_dois": [
      "10.1038/s41586-023-06812-z"
    ],
    "effect_size_source_sentence": "we generated a comprehensive cell atlas of more than 5,000 transcriptionally distinct cell clusters, belonging to more than 300 major cell types, in the whole mouse brain"
  },
  "section_id": "section_15",
  "source_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence/blob/79ce062d54a924ce05953ec90aa9d26044d2b48f/evidence/section_15_evidence_package.json",
  "effect_size": ">10 million cells; >5,000 clusters; >300 major cell types",
  "review_repo": "ComputationalReviewRecurrence",
  "section_ref": "wiki_page:computationalreviewrecurrence-15-methods-limits",
  "source_kind": "review_finding",
  "source_path": "evidence/section_15_evidence_package.json",
  "source_refs": [
    "paper:paper-748279add05a"
  ],
  "source_span": "Here we imaged a panel of more than 1,100 genes in approximately 10 million cells across the entire adult mouse brains using multiplexed error-robust fluorescence in situ hybridization12 and performed spatially resolved, single-cell expression profiling at the whole-transcriptome scale by integrating multiplexed error-robust fluorescence in situ hybridization and single-cell RNA sequencing data.",
  "study_system": "Adult mouse whole brain (MERFISH + scRNA-seq atlas, BICCN-affiliated)",
  "evidence_refs": [
    {
      "ref": "paper:paper-748279add05a"
    }
  ],
  "section_title": "15. Methodological limits and emerging tools — what current mouse-cortex tools cannot yet measure about E→E recurrence (subthreshold network activity, fast plasticity in vivo, millimetre-scale dynamic connectomes), and what is on the near horizon",
  "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"
  },
  "evidence_summary": "MERFISH + scRNA-seq integration; >10 million cells; >5,000 clusters in >300 major cell types; CCF-registered.",
  "review_bundle_ref": "analysis_bundle:ab-d9c479db9be9",
  "replication_status": "paired-with-Yao2023",
  "review_package_ref": "analysis_bundle:ab-d9c479db9be9",
  "source_artifact_ref": "wiki_page:computationalreviewrecurrence-15-methods-limits",
  "origin_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence/blob/79ce062d54a924ce05953ec90aa9d26044d2b48f/evidence/section_15_evidence_package.json",
  "commit_sha": "79ce062d54a924ce05953ec90aa9d26044d2b48f",
  "created_by": "persona-jerome-lecoq-gbo-neuroscience",
  "repository_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence"
}