{
 "index_columns": {
  "gsm": "GEO sample (canonical GSM of its content group)",
  "gse": "all GEO series listing the GSM, joined with '+'; the split is computed on this string",
  "published_gse": "series folder of the sample: samples/<published_gse>/<gsm>",
  "source_pipeline": "sda-all (agent standardization, independent scorer) or hesrt (H&E Visium/ST, human review)",
  "source_release": "SDA-All scorer version of the batch, sda-all-gap-20261009, or hesrt-v1.3",
  "platform": "harmonized platform",
  "technology": "technology as written by the authors",
  "organism": "as written in GEO",
  "tissue": "as written in GEO",
  "observation_unit": "spot / bin / cell / bead",
  "n_obs": "observations",
  "n_vars": "features",
  "expression_state": "counts (integer X) / non-integer / unknown (SDA-All: as declared and scored)",
  "verification": "VERIFIED / ATTESTED (SDA-All scorer) or human_visual_review (HESRT)",
  "expression_sha256": "SHA256 of the sample's spatial.h5ad",
  "coordinate_units": "units of obsm['spatial']: um / pixel / native_grid / unstated",
  "um_basis": "verified / declared_unverified / platform_constant / unresolved",
  "um_per_unit": "micrometres per coordinate unit when known",
  "has_spatial_um": "obsm['spatial_um'] present (micrometre copy of non-um coordinates)",
  "has_image": "image.tif present",
  "image_stain": "stain of image.tif ('(heuristic)' = pixel-only call)",
  "image_stain_basis": "basis of the stain label",
  "image_um_per_px": "micrometres per image.tif pixel when known",
  "image_registration": "VERIFIED / PARTIAL / UNRESOLVED / FAILED / ABSENT (modality acceptance), WITHHELD (HESRT review FAIL: no image delivered), HESRT_HUMAN_REVIEW, empty = no registrable image",
  "image_sha256": "SHA256 of image.tif",
  "segmentation": "cell / nucleus boundary acceptance (sources in sample.json)",
  "molecules": "molecule table acceptance (sources in sample.json)",
  "molecules_use": "positions_only: molecules without usable cell IDs",
  "flags": "units_unstated / attested / summary_features_in_matrix / hesrt_review_fail / hesrt_fail_image_released / image_partial_coverage / image_review_fail",
  "qc_flags": "deposit QC flags (annotation only)",
  "drop_features": "features to drop before use",
  "review_decision": "latest author review of this expression file: PASS / FAIL / UNSURE",
  "review_category": "review category",
  "review_notes": "review notes",
  "content_group": "independence unit",
  "group_kind": "cross_gse_redeposit / library_alias",
  "aliases": "GSMs with identical content not listed as rows",
  "split": "train / val / test by series",
  "sample_dir": "samples/<published_gse>/<gsm>"
 },
 "sample_json": {
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "sda-release-sample-1",
  "type": "object",
  "additionalProperties": false,
  "required": [
   "schema",
   "release_id",
   "gsm",
   "gse",
   "published_gse",
   "metadata",
   "expression",
   "coordinates",
   "image",
   "segmentation",
   "molecules",
   "quality",
   "dedup",
   "split",
   "provenance"
  ],
  "properties": {
   "schema": {
    "const": "sda-release-sample-1"
   },
   "release_id": {
    "type": "string"
   },
   "gsm": {
    "type": "string",
    "pattern": "^GSM[0-9]+$"
   },
   "gse": {
    "type": "array",
    "items": {
     "type": "string",
     "pattern": "^GSE[0-9]+$"
    },
    "minItems": 1
   },
   "published_gse": {
    "type": "string",
    "pattern": "^GSE[0-9]+$"
   },
   "metadata": {
    "type": "object",
    "required": [
     "organism",
     "tissue",
     "platform",
     "technology"
    ],
    "properties": {
     "organism": {
      "type": [
       "string",
       "null"
      ]
     },
     "tissue": {
      "type": [
       "string",
       "null"
      ]
     },
     "platform": {
      "type": "string"
     },
     "technology": {
      "type": [
       "string",
       "null"
      ]
     },
     "fields": {
      "type": "object"
     },
     "field_sources": {
      "type": "object"
     }
    }
   },
   "expression": {
    "type": "object",
    "additionalProperties": false,
    "required": [
     "file",
     "sha256",
     "n_obs",
     "n_vars",
     "state",
     "observation_unit",
     "verification"
    ],
    "properties": {
     "file": {
      "const": "spatial.h5ad"
     },
     "sha256": {
      "type": "string",
      "pattern": "^[0-9a-f]{64}$"
     },
     "n_obs": {
      "type": "integer",
      "minimum": 1
     },
     "n_vars": {
      "type": "integer",
      "minimum": 1
     },
     "state": {
      "type": "string"
     },
     "observation_unit": {
      "type": [
       "string",
       "null"
      ]
     },
     "verification": {
      "type": "string"
     }
    }
   },
   "coordinates": {
    "type": "object",
    "additionalProperties": false,
    "required": [
     "obsm_key",
     "units",
     "um_basis",
     "spatial_um"
    ],
    "properties": {
     "obsm_key": {
      "const": "spatial"
     },
     "units": {
      "enum": [
       "mm",
       "native_grid",
       "nm",
       "pixel",
       "um",
       "unstated"
      ]
     },
     "um_basis": {
      "enum": [
       "declared_unverified",
       "platform_constant",
       "unresolved",
       "verified"
      ]
     },
     "um_per_unit": {
      "type": [
       "number",
       "null"
      ]
     },
     "um_basis_detail": {
      "type": [
       "string",
       "null"
      ]
     },
     "spatial_um": {
      "type": "boolean"
     }
    }
   },
   "image": {
    "oneOf": [
     {
      "type": "null"
     },
     {
      "type": "object",
      "additionalProperties": false,
      "required": [
       "file",
       "sha256",
       "shape",
       "dtype",
       "channels",
       "stain",
       "um_per_px",
       "spatial_to_pixel",
       "registration",
       "inside_fraction",
       "source"
      ],
      "properties": {
       "file": {
        "const": "image.tif"
       },
       "sha256": {
        "type": "string",
        "pattern": "^[0-9a-f]{64}$"
       },
       "shape": {
        "type": "array",
        "items": {
         "type": "integer"
        },
        "minItems": 2,
        "maxItems": 2
       },
       "dtype": {
        "enum": [
         "uint8",
         "uint16"
        ]
       },
       "channels": {
        "type": "array",
        "items": {
         "type": "string"
        },
        "minItems": 1
       },
       "stain": {
        "type": [
         "string",
         "null"
        ]
       },
       "stain_basis": {
        "type": [
         "string",
         "null"
        ]
       },
       "um_per_px": {
        "type": [
         "number",
         "null"
        ]
       },
       "spatial_to_pixel": {
        "type": "array",
        "minItems": 3,
        "maxItems": 3,
        "items": {
         "type": "array",
         "items": {
          "type": "number"
         },
         "minItems": 3,
         "maxItems": 3
        }
       },
       "registration": {
        "type": "string"
       },
       "review": {
        "type": [
         "string",
         "null"
        ]
       },
       "inside_fraction": {
        "type": "number",
        "minimum": 0,
        "maximum": 1
       },
       "source": {
        "type": "array"
       }
      }
     }
    ]
   },
   "segmentation": {
    "type": [
     "object",
     "null"
    ]
   },
   "molecules": {
    "type": [
     "object",
     "null"
    ]
   },
   "quality": {
    "type": "object",
    "required": [
     "flags",
     "qc_flags",
     "drop_features",
     "review"
    ],
    "properties": {
     "flags": {
      "type": "array",
      "items": {
       "type": "string"
      }
     },
     "qc_flags": {
      "type": "array",
      "items": {
       "type": "string"
      }
     },
     "drop_features": {
      "type": "array",
      "items": {
       "type": "string"
      }
     },
     "review": {
      "type": [
       "object",
       "null"
      ]
     }
    }
   },
   "dedup": {
    "type": "object",
    "required": [
     "content_group",
     "group_kind",
     "aliases"
    ],
    "properties": {
     "content_group": {
      "type": "string"
     },
     "group_kind": {
      "type": [
       "string",
       "null"
      ]
     },
     "aliases": {
      "type": "array",
      "items": {
       "type": "string"
      }
     }
    }
   },
   "split": {
    "enum": [
     "train",
     "val",
     "test"
    ]
   },
   "provenance": {
    "type": "object",
    "required": [
     "pipeline",
     "source_release",
     "files"
    ],
    "properties": {
     "pipeline": {
      "enum": [
       "sda-all",
       "hesrt"
      ]
     },
     "source_release": {
      "type": "string"
     },
     "files": {
      "type": "array",
      "items": {
       "type": "object",
       "required": [
        "role",
        "path"
       ],
       "properties": {
        "role": {
         "type": "string"
        },
        "path": {
         "type": "string"
        },
        "sha256": {
         "type": [
          "string",
          "null"
         ]
        }
       }
      }
     }
    }
   }
  }
 },
 "sample_folder": [
  "image.tif",
  "sample.json",
  "spatial.h5ad"
 ]
}