Hello, we have downloaded the HE slides images from Molecular Characterization Initiative of the National Cancer Institute’s Childhood Cancer Data Initiative. However, we didn’t find the clinical or genetic information of these slides. Could you please kindly share how we can get and correlate these clinical informations with slide images? Thanks!
@beatrice thank you for reaching out with this question!
In addition to the resources shared above by @dclunie, which you should most definitely explore, a subset of clinical data is available directly in IDC along with the images. You are not the first one asking this question, and I will follow up with the details. I need some time to prepare that detailed response.
Note that we do not have any genetic/genomic information about IDC. The only way I am aware of to access it right now is through the resources mentioned by David.
@beatrice I updated this notebook to include an example how to access metadata describing anatomic structure and patient diagnosis, which for the CCDI-MCI collection is included in DICOM attributes: IDC-Tutorials/notebooks/pathomics/slide_microscopy_metadata_search.ipynb at master · ImagingDataCommons/IDC-Tutorials · GitHub
In short, idc-index python package, as of version 0.7.4, includes DICOM information from the AdmittingDiagnosesSequence as well as PrimaryAnatomicStructure in the sm_index table. The tutorial notebook referenced above demonstrates how to use idc-index for subsetting the slides, and how to download the selection.
If you are not a programmer, and you need to select slides by diagnosis without writing any code, please let us know!