spider2/lite/external/dicom_dataset_selection.md

Detailed requirements include:

• The slides must belong to the TCGA-LUAD or TCGA-LUSC collections;
• The slides must be JPEG or JPEG2000 compressed;
• The slides must be digital images and exclude non-volume ones;
• The slides must contain either normal (17621005) or tumor (86049000) tissue, identified by specific DICOM codes;
• The slides must be prepared using the "Tissue freezing medium" embedding method;

With respect to the output, it should contain the following basic metadata and attributes related to slide microscopy images. Concretely,

• digital slide ID: unique numeric identifier of a digital slide, i.e., a digital image of a physical slide;
• case ID: unique numeric identifier of the study in the context of which the ditial slide was created;
• physical slide ID: unique numeric identifier of the physical slide as prepared in the wet lab;
• patient ID: unique numeric identifier of the patient from whose tissue the physical slide was obtained;
• collection ID: numeric or character sequence describing the dataset the physical slide is part of;
• instance ID: universally unique identifier of the DICOM instance;
• GCS URL: how to access the DICOM file;
• width/height: image width and height in pixels, respectively;
• pixel spacing: image pixel spacing in mm/px;
• compression type (either value jpeg, jpeg2000, or other).

And the target two labels are:

• tissue_type: either normal or tumor;
• cancer_subtype: either luad or lscc. Sort the results according to instance ID in ascending order.