sm_index_schema.json

{
  "table_description": "This table contains metadata about the slide microscopy (SM) series available in IDC. Each row corresponds to a DICOM series, and contains attributes specific to SM series, such as the pixel spacing at the maximum resolution layer, the power of the objective lens used to digitize the slide, and the anatomic location from where the imaged specimen was collected. This table can be joined with the main index table using the `SeriesInstanceUID` column.",
  "columns": [
    {
      "name": "SeriesInstanceUID",
      "type": "STRING",
      "mode": "NULLABLE",
      "description": ""
    },
    {
      "name": "ContainerIdentifier",
      "type": "STRING",
      "mode": "NULLABLE",
      "description": "identifier of the container (e.g., glass slide) holding the specimen from DICOM ContainerIdentifier attribute"
    },
    {
      "name": "embeddingMedium_CodeMeaning",
      "type": "STRING",
      "mode": "REPEATED",
      "description": "embedding medium CodeMeaning from DICOM SpecimenPreparationSequence in SpecimenDescriptionSequence"
    },
    {
      "name": "embeddingMedium_code_designator_value_str",
      "type": "STRING",
      "mode": "REPEATED",
      "description": "embedding medium code tuple from DICOM SpecimenPreparationSequence in SpecimenDescriptionSequence"
    },
    {
      "name": "tissueFixative_CodeMeaning",
      "type": "STRING",
      "mode": "REPEATED",
      "description": "tissue fixative CodeMeaning from DICOM SpecimenPreparationSequence in SpecimenDescriptionSequence"
    },
    {
      "name": "tissueFixative_code_designator_value_str",
      "type": "STRING",
      "mode": "REPEATED",
      "description": "tissue fixative code tuple from DICOM SpecimenPreparationSequence in SpecimenDescriptionSequence"
    },
    {
      "name": "staining_usingSubstance_CodeMeaning",
      "type": "STRING",
      "mode": "REPEATED",
      "description": "staining substances CodeMeaning from DICOM SpecimenPreparationSequence in SpecimenDescriptionSequence"
    },
    {
      "name": "staining_usingSubstance_code_designator_value_str",
      "type": "STRING",
      "mode": "REPEATED",
      "description": "staining substances code tuple from DICOM SpecimenPreparationSequence in SpecimenDescriptionSequence"
    },
    {
      "name": "min_PixelSpacing_2sf",
      "type": "FLOAT",
      "mode": "NULLABLE",
      "description": "pixel spacing in mm at the maximum resolution layer, rounded to 2 significant figures, derived from DICOM PixelSpacing attribute"
    },
    {
      "name": "max_TotalPixelMatrixColumns",
      "type": "INTEGER",
      "mode": "NULLABLE",
      "description": "width of the image at the maximum resolution from DICOM TotalPixelMatrixColumns attribute"
    },
    {
      "name": "max_TotalPixelMatrixRows",
      "type": "INTEGER",
      "mode": "NULLABLE",
      "description": "height of the image at the maximum resolution from DICOM TotalPixelMatrixRows attribute"
    },
    {
      "name": "ObjectiveLensPower",
      "type": "INTEGER",
      "mode": "NULLABLE",
      "description": "power of the objective lens from DICOM ObjectiveLensPower attribute in OpticalPathSequence"
    },
    {
      "name": "primaryAnatomicStructure_code_designator_value_str",
      "type": "STRING",
      "mode": "NULLABLE",
      "description": "anatomic location code tuple from DICOM PrimaryAnatomicStructureSequence in SpecimenDescriptionSequence"
    },
    {
      "name": "primaryAnatomicStructure_CodeMeaning",
      "type": "STRING",
      "mode": "NULLABLE",
      "description": "anatomic location CodeMeaning from DICOM PrimaryAnatomicStructureSequence in SpecimenDescriptionSequence"
    },
    {
      "name": "primaryAnatomicStructureModifier_code_designator_value_str",
      "type": "STRING",
      "mode": "NULLABLE",
      "description": "specimen modifier code tuple from DICOM PrimaryAnatomicStructureModifierSequence (when available)"
    },
    {
      "name": "primaryAnatomicStructureModifier_CodeMeaning",
      "type": "STRING",
      "mode": "NULLABLE",
      "description": "specimen modifier CodeMeaning from DICOM PrimaryAnatomicStructureModifierSequence (when available)"
    },
    {
      "name": "illuminationType_code_designator_value_str",
      "type": "STRING",
      "mode": "NULLABLE",
      "description": "illumination type code tuple from DICOM IlluminationTypeCodeSequence in OpticalPathSequence"
    },
    {
      "name": "illuminationType_CodeMeaning",
      "type": "STRING",
      "mode": "NULLABLE",
      "description": "illumination type CodeMeaning from DICOM IlluminationTypeCodeSequence in OpticalPathSequence"
    },
    {
      "name": "admittingDiagnosis_code_designator_value_str",
      "type": "STRING",
      "mode": "NULLABLE",
      "description": "admitting diagnosis code tuple from DICOM AdmittingDiagnosesCodeSequence (when available)"
    },
    {
      "name": "admittingDiagnosis_CodeMeaning",
      "type": "STRING",
      "mode": "NULLABLE",
      "description": "admitting diagnosis CodeMeaning from DICOM AdmittingDiagnosesCodeSequence (when available)"
    }
  ]
}