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column_descriptions.md

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Metadata attributes in idc-index's index tables

index

The following is the list of the columns included in index. You can use those to select cohorts and subsetting data. index is series-based, i.e, it has one row per DICOM series.

  • non-DICOM attributes assigned/curated by IDC:

    • collection_id: short string with the identifier of the collection the series belongs to
    • analysis_result_id: this string is not empty if the specific series is part of an analysis results collection; analysis results can be added to a given collection over time
    • source_DOI: Digital Object Identifier of the dataset that contains the given series; note that a given collection can include one or more DOIs, since analysis results added to the collection would typically have independent DOI values!
    • instanceCount: number of files in the series (typically, this matches the number of slices in cross-sectional modalities)
    • license_short_name: short name of the license that governs the use of the files corresponding to the series
    • series_aws_url: location of the series files in a public AWS bucket
    • series_size_MB: total disk size needed to store the series

  • DICOM attributes extracted from the files

    • PatientID: identifier of the patient
    • PatientAge and PatientSex: attributes containing patient age and sex
    • StudyInstanceUID: unique identifier of the DICOM study
    • StudyDescription: textual description of the study content
    • StudyDate: date of the study (note that those dates are shifted, and are not real dates when images were acquired, to protect patient privacy)
    • SeriesInstanceUID: unique identifier of the DICOM series
    • SeriesDate: date when the series was acquired
    • SeriesDescription: textual description of the series content
    • SeriesNumber: series number
    • BodyPartExamined: body part imaged
    • Modality: acquisition modality
    • Manufacturer: manufacturer of the equipment that generated the series
    • ManufacturerModelName: model name of the equipment

sm_index

The following is the list of the columns included in sm_index. sm_index is series-based, i.e, it has one row per DICOM series, but only includes series with slide microscopy data.

  • DICOM attributes extracted from the files:
    • SeriesInstanceUID: unique identifier of the DICOM series: one DICOM series = one slide
    • embeddingMedium: describes in what medium the slide was embedded before the image was obtained
    • tissueFixative: describes tissue fixatives used before the image was obtained
    • staining_usingSubstance: describes staining steps the specimen underwent before the image was obtained
    • max_TotalPixelMatrixColumns: width of the image at the maximum resolution
    • max_TotalMatrixRows: height of the image at the maximum resolution
    • min_PixelSpacing_2sf: pixel spacing in mm at the maximum resolution layer, rounded to 2 significant figures
    • ObjectiveLensPower: power of the objective lens of the equipment used to digitize the slide
    • primaryAnatomicStructure: anatomic location from where the imaged specimen was collected
    • primaryAnatomicStructureModifier: additional characteristics of the specimen, such as whether it is a tumor or normal tissue
    • illuminationType: specifies the type of illumination used when obtaining the image

In case of embeddingMedium, tissueFixative, staining_usingSubstance, primaryAnatomicStructure, primaryAnatomicStructureModifier and illuminationType the attributes exist with suffix _code_designator_value_str and _CodeMeaning, which indicates whether the column contains CodeSchemeDesignator and CodeValue, or CodeMeaning. If this is new to you, a brief explanation on the three-value based coding scheme in DICOM can be found at https://learn.canceridc.dev/dicom/coding-schemes.

sm_instance_index

The following is the list of the columns included in sm_instance_index. sm_instance_index is instance-based, i.e, it has one row per DICOM instance (pyramid level of a slide, plus potentially thumbnail or label images), but only includes DICOM instances of the slide microscopy modality.

  • DICOM attributes extracted from the files:

    • SOPInstanceUID: unique identifier of the DICOM instance: one DICOM instance = one level/label/thumbnail image of the slide
    • SeriesInstanceUID: unique identifier of the DICOM series: one DICOM series = one slide
    • embeddingMedium: describes in what medium the slide was embedded before the image was obtained
    • tissueFixative: describes tissue fixatives used before the image was obtained
    • staining_usingSubstance: describes staining steps the specimen underwent before the image was obtained
    • max_TotalPixelMatrixColumns: width of the image at the maximum resolution
    • max_TotalMatrixRows: height of the image at the maximum resolution
    • PixelSpacing_0: pixel spacing in mm
    • ImageType: specifies further characteristics of the image in a list, including as the third value whether it is a VOLUME, LABEL, OVERVIEW or THUMBNAIL image.
    • TransferSyntaxUID: specifies the encoding scheme used for the image data
    • instance_size: specifies the DICOM instance's size in bytes

  • non-DICOM attributes assigned/curated by IDC:

    • crdc_instance_uuid: globally unique, versioned identifier of the DICOM instance

In case of embeddingMedium, tissueFixative, and staining_usingSubstance the attributes exist with suffix _code_designator_value_str and _CodeMeaning, which indicates whether the column contains CodeSchemeDesignator and CodeValue, or CodeMeaning. If this is new to you, a brief explanation on the three-value based coding scheme in DICOM can be found at https://learn.canceridc.dev/dicom/coding-schemes.