Version history

{
  "scope": "Whole mouse brain atlas (extended CCFv3)",
  "claim_text": "The Blue Brain CCFv3 augmented atlas extends Allen's CCFv3 to fully annotate olfactory bulb, cerebellum, medulla and central nervous system regions and aligns 734 Nissl-stained brains to produce an averaged 10-µm Nissl template — the registration substrate on which cell-type counts and projection-target labels in mouse-cortex E→E synthesis depend.",
  "raw_fields": {
    "n": 734,
    "doi": "10.1162/imag_a_00565",
    "claim": "The Blue Brain CCFv3 augmented atlas extends Allen's CCFv3 to fully annotate olfactory bulb, cerebellum, medulla and central nervous system regions and aligns 734 Nissl-stained brains to produce an averaged 10-µm Nissl template — the registration substrate on which cell-type counts and projection-target labels in mouse-cortex E→E synthesis depend.",
    "cite_key": "Piluso2025",
    "evidence": "Atlas extension covering previously missing regions; 734 brains aligned for averaged Nissl template; first in silico whole-CNS cell-distribution model.",
    "effect_size": "734 Nissl brains aligned; 10 µm averaged template",
    "text_access": "fulltext",
    "study_system": "Whole mouse brain atlas (extended CCFv3)",
    "argument_role": "supporting",
    "replication_status": "atlas-resource",
    "claim_source_sentence": "we developed the Blue Brain Project (BBP) CCFv3 augmented atlas (CCFv3BBP), which includes a fully annotated mouse brain and an improved Nissl-stained reference volume aligned with the CCFv3BBP. This enhanced atlas also features the central nervous system annotation.",
    "source_provenance_status": "ok",
    "replication_evidence_dois": [],
    "effect_size_source_sentence": "we aligned 734 Nissl-stained brains to generate an average Nissl template at 10 µm resolution."
  },
  "section_id": "section_16",
  "source_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence/blob/79ce062d54a924ce05953ec90aa9d26044d2b48f/evidence/section_16_evidence_package.json",
  "effect_size": "734 Nissl brains aligned; 10 µm averaged template",
  "review_repo": "ComputationalReviewRecurrence",
  "section_ref": "wiki_page:computationalreviewrecurrence-16-synthesis",
  "source_kind": "review_finding",
  "source_path": "evidence/section_16_evidence_package.json",
  "source_refs": [
    "paper:paper-3cf435c26092"
  ],
  "source_span": "we developed the Blue Brain Project (BBP) CCFv3 augmented atlas (CCFv3BBP), which includes a fully annotated mouse brain and an improved Nissl-stained reference volume aligned with the CCFv3BBP. This enhanced atlas also features the central nervous system annotation.",
  "study_system": "Whole mouse brain atlas (extended CCFv3)",
  "evidence_refs": [
    {
      "ref": "paper:paper-3cf435c26092"
    }
  ],
  "section_title": "16. Synthesis — which computational claims the mouse-cortex E→E empirical record actually supports, where the bottleneck observations are, and what an inhibition-free, single-species, basic-research analytic framing misses",
  "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": "Atlas extension covering previously missing regions; 734 brains aligned for averaged Nissl template; first in silico whole-CNS cell-distribution model.",
  "review_bundle_ref": "analysis_bundle:ab-d9c479db9be9",
  "replication_status": "atlas-resource",
  "review_package_ref": "analysis_bundle:ab-d9c479db9be9",
  "source_artifact_ref": "wiki_page:computationalreviewrecurrence-16-synthesis",
  "origin_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence/blob/79ce062d54a924ce05953ec90aa9d26044d2b48f/evidence/section_16_evidence_package.json",
  "commit_sha": "79ce062d54a924ce05953ec90aa9d26044d2b48f",
  "created_by": "persona-jerome-lecoq-gbo-neuroscience",
  "repository_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence"
}