{
  "schemaVersion": "finger-atlas-v4-cortex-sources/1",
  "reviewedOn": "2026-10-15",
  "scope": {
    "anatomy": "Paired left precentral (M1) and postcentral (S1) gyri shown as coronal-orientation cut faces in the existing Finger Pathway Atlas coordinate system.",
    "layers": "Six isocortical layers are present in both sections. M1 is modeled as agranular with a very thin or indistinct layer IV and expanded pyramidal layers; S1 is modeled as granular with a prominent thalamorecipient layer IV.",
    "microstructure": "Twelve H01 source neurite components with original object IDs and source-layer labels are transplanted rigidly to both M1/S1 samples. H01 is temporal cortex. Remaining cells and glial context are representative models; positions, new axon continuations and region assignments are not measured M1/S1 tissue or mapped synapses.",
    "tracts": "No DKI acquisition has been fitted. Primary DKI references provide a proposed workflow for voxel-scale orientation peaks and anatomical tracking. Rendered individual axon cylinders, spacing, radii and endpoints are modeled; these are not DKI-derived observations.",
    "mri": "MRI-style illustrative coronal tissue sections at two separate anterior-posterior planes, not a patient MRI, a segmented scan, or a single slice placing M1 and S1 side by side."
  },
  "implementation": {
    "m1": {
      "label": "Primary motor cortex / precentral gyrus",
      "corticalThicknessPriorMm": 3.4,
      "layerFractions": [
        0.08,
        0.1,
        0.25,
        0.05,
        0.26,
        0.26
      ],
      "specialization": "Agranular cortex; layer IV is retained as a thin six-layer bookkeeping band rather than claimed as a sharply defined granular layer. Layer V has the largest representative corticofugal somata.",
      "originMm": [
        41,
        351,
        0
      ]
    },
    "s1": {
      "label": "Primary somatosensory cortex / postcentral gyrus",
      "corticalThicknessPriorMm": 2.2,
      "layerFractions": [
        0.08,
        0.11,
        0.24,
        0.17,
        0.18,
        0.22
      ],
      "specialization": "Granular cortex; layer IV is expanded as the principal thalamorecipient band.",
      "originMm": [
        43,
        354,
        -21
      ]
    },
    "lod": {
      "gross": "Only the left source precentral and postcentral gyri are rendered in the body view.",
      "laminar": "Two separate coronal cameras keep all six layers of both samples visible at the same physical magnification.",
      "cellular": "620 distinct sample cells, including 24 transplanted instances of twelve H01 source trees, connected cylindrical arbors and projection continuations.",
      "visibilityNote": "Source and cell radii remain physical; optional axonal radius padding improves visibility. Counts and spacing are representative, not stereological measurements."
    },
    "dkiRules": [
      "Use local orientation-distribution peaks and cortical surface normals as direction priors.",
      "Render multiple nearby streamlines as an uncertainty envelope rather than a single asserted tract.",
      "Terminate thalamocortical orientation families preferentially in S1 layer IV and originate corticofugal families preferentially in M1 layer V.",
      "Include short association U-fiber orientation under the central-sulcus interval.",
      "Do not infer axon identity, synapse identity, conduction direction or exact endpoints from DKI alone."
    ],
    "sourceImplementation": [
      "src/lib/finger-atlas-v4/cortical-model.mjs",
      "src/lib/finger-atlas-v4/cortical-sections.mjs",
      "src/lib/finger-atlas-v4/tubes.mjs"
    ],
    "dkiRulesStatus": "Proposed modeling guidance, not a fitted diffusion-data result.",
    "h01Pack": "/assets/finger-pathway-atlas/v4/h01/reference-neurites.json"
  },
  "references": [
    {
      "id": "h01-science-2024",
      "title": "A petavoxel fragment of human cerebral cortex reconstructed at nanoscale resolution",
      "authors": "Shapson-Coe et al.",
      "year": 2024,
      "modality": "serial-section electron microscopy / connectomics",
      "doi": "10.1126/science.adk4858",
      "url": "https://doi.org/10.1126/science.adk4858",
      "usedFor": [
        "six-layer reference morphology",
        "proofread neurite trees",
        "human cortical ultrastructure context"
      ],
      "boundary": "The H01 specimen is temporal cortex from surgical tissue, not primary motor or primary somatosensory cortex."
    },
    {
      "id": "h01-google-release",
      "title": "A Browsable Petascale Reconstruction of the Human Cortex",
      "organization": "Google Research / Lichtman laboratory",
      "year": 2021,
      "modality": "public H01 data release",
      "url": "https://h01-release.storage.googleapis.com/data.html",
      "usedFor": [
        "dataset scale",
        "all-layer inspection concept"
      ],
      "boundary": "Twelve proofread connected SWC components are copied with source IDs, anisotropic position calibration, physical radii, license and hashes; not a complete H01 connectome or EM membrane segmentation."
    },
    {
      "id": "bigbrain-layers-2020",
      "title": "BigBrain 3D atlas of cortical layers: Cortical and laminar thickness gradients diverge in sensory and motor cortices",
      "authors": "Wagstyl et al.",
      "year": 2020,
      "modality": "20-micrometer 3D histology / six-layer segmentation",
      "doi": "10.1371/journal.pbio.3000678",
      "url": "https://doi.org/10.1371/journal.pbio.3000678",
      "usedFor": [
        "six-layer surface-normal construction",
        "motor-versus-sensory laminar differentiation",
        "coronal histological registration logic"
      ],
      "boundary": "Regional histological reference retained from PR #279; current numerical fractions are model priors, not sampled BigBrain surface values."
    },
    {
      "id": "bigbrain-layers-2018",
      "title": "Mapping Cortical Laminar Structure in the 3D BigBrain",
      "authors": "Wagstyl et al.",
      "year": 2018,
      "modality": "3D histology / laminar mapping",
      "doi": "10.1093/cercor/bhy074",
      "url": "https://doi.org/10.1093/cercor/bhy074",
      "usedFor": [
        "layer-boundary construction along folded cortex",
        "pial-to-white-matter depth coordinates"
      ],
      "boundary": "Regional histological reference retained from PR #279; current numerical fractions are model priors, not sampled BigBrain surface values."
    },
    {
      "id": "dki-original-2005",
      "title": "Diffusional kurtosis imaging: The quantification of non-Gaussian water diffusion by means of magnetic resonance imaging",
      "authors": "Jensen et al.",
      "year": 2005,
      "modality": "diffusion kurtosis MRI",
      "doi": "10.1002/mrm.20508",
      "url": "https://doi.org/10.1002/mrm.20508",
      "usedFor": [
        "non-Gaussian diffusion basis",
        "kurtosis-informed uncertainty"
      ]
    },
    {
      "id": "dki-odf-2008",
      "title": "Estimation of the orientation distribution function from diffusional kurtosis imaging",
      "authors": "Lazar et al.",
      "year": 2008,
      "modality": "DKI orientation distribution function",
      "doi": "10.1002/mrm.21725",
      "url": "https://doi.org/10.1002/mrm.21725",
      "usedFor": [
        "multiple orientation peaks",
        "probabilistic streamline fan construction"
      ]
    },
    {
      "id": "cortical-diffusion-orientation-2013",
      "title": "Surface based analysis of diffusion orientation for identifying architectonic domains in the in vivo human cortex",
      "authors": "McNab et al.",
      "year": 2013,
      "modality": "high-resolution diffusion MRI",
      "doi": "10.1016/j.neuroimage.2012.11.065",
      "url": "https://doi.org/10.1016/j.neuroimage.2012.11.065",
      "usedFor": [
        "surface-normal-relative intracortical orientation",
        "M1/S1 orientation transition",
        "radial-versus-tangential cortical priors"
      ],
      "boundary": "Diffusion orientation is a voxel-scale signal and is not rendered as an axon-resolved measurement."
    },
    {
      "id": "dki-white-matter-2011",
      "title": "White matter characterization with diffusional kurtosis imaging",
      "authors": "Fieremans et al.",
      "year": 2011,
      "modality": "DKI white-matter modeling",
      "doi": "10.1016/j.neuroimage.2011.06.006",
      "url": "https://doi.org/10.1016/j.neuroimage.2011.06.006",
      "usedFor": [
        "white-matter microstructural uncertainty",
        "bundle-envelope interpretation"
      ]
    },
    {
      "id": "dki-fiber-orientation-2016",
      "title": "Mapping the orientation of white matter fiber bundles: a comparative study of diffusion tensor imaging, diffusional kurtosis imaging, and diffusion spectrum imaging",
      "authors": "Glenn et al.",
      "year": 2016,
      "modality": "comparative diffusion tract orientation",
      "doi": "10.3174/ajnr.A4714",
      "url": "https://doi.org/10.3174/ajnr.A4714",
      "usedFor": [
        "crossing-fiber orientation caveats",
        "DKI-versus-tensor direction prior"
      ]
    },
    {
      "id": "dki-odf-2014",
      "title": "Leading non-Gaussian corrections for diffusion orientation distribution function",
      "doi": "10.1002/nbm.3053",
      "url": "https://doi.org/10.1002/nbm.3053",
      "usedFor": [
        "proposed DKI tract-orientation workflow; no fitted dataset"
      ]
    },
    {
      "id": "dki-tractography-2015",
      "title": "Optimization of white matter fiber tractography with diffusional kurtosis imaging",
      "doi": "10.1002/nbm.3374",
      "url": "https://doi.org/10.1002/nbm.3374",
      "usedFor": [
        "proposed DKI tract-orientation workflow; no fitted dataset"
      ]
    }
  ]
}