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include column descriptions from separate file
minor text changes updated ImageType description check if include command works now Moved section introducing indices of idc-index into README Test to see if docs are build correctly Docs: Added separate page for column description of indices and linked to it from README. removed test fixed link removed doubled text adapted toctree to generate column_descriptions.html corrected toctree another try next try a test probably solved added title and sections
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| # Metadata attributes in `idc-index`'s index tables | ||
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| ## `index` | ||
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| 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. | ||
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| - non-DICOM attributes assigned/curated by IDC: | ||
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| - `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 | ||
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| - 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 | ||
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| ## `sm_index` | ||
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| 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. | ||
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| - 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 | ||
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| 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. | ||
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| ## `sm_instance_index` | ||
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| 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. | ||
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| - DICOM attributes extracted from the files: | ||
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| - `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 | ||
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| - non-DICOM attributes assigned/curated by IDC: | ||
| - `crdc_instance_uuid`: globally unique, versioned identifier of the DICOM | ||
| instance | ||
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| 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. |
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