Filtering to find all H&E images in IDC

Hello, I have an interest in seeing a list of all the H&E images in IDC. Is this possible?

Here’s what I’ve tried. I’ve used the exploration tools at the portal (https://portal.imaging.datacommons.cancer.gov/explore/) and was able to narrow down by selecting “Slide Microscopy” from Modality and “Brightfield illumination” from Illumination Type. Is there any further capability to filter specifically for H&E stained images? I have also tried the idc-index python package but again it is not clear to me whether there are any means to filter to the H&E stain.

Thank you very much for any suggestions!

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You cannot do this in the portal, but it is definitely possible with idc-index.

Take a look at this tutorial notebook: IDC-Tutorials/notebooks/pathomics/slide_microscopy_metadata_search.ipynb at master · ImagingDataCommons/IDC-Tutorials · GitHub.

idc-index sm_index table staining_usingSubstance group of attributes is what you need:

  • staining_usingSubstance_CodeMeaning: human-readable description of the stain
  • staining_usingSubstance_code_designator_value_str: colon-separated coding scheme designator and code value (typically, those code tuples will be coming from SNOMED-CT).

For the H&E slides, you will see the following, which you can use for filtering:

  • staining_usingSubstance_CodeMeaning: “[water soluble eosin stain, hematoxylin stain]” (in this or reverse order)
  • staining_usingSubstance_code_designator_value_str: “[SCT:36879007, SCT:12710003]” (you can look up what those codes mean and where they fit in the ontology of SNOMED-CT using this URL template: http://snomed.info/id/<code>, as in http://snomed.info/id/12402003 and http://snomed.info/id/36879007.

Note that in the source DICOM metadata, eosin and hematoxylin stains are siblings and are captured separately. In sm_index, these are aggregated into array to simplify access.

I hope this answers your question?

Did you see the tutorial notebook I mentioned earlier? If not, I recommend you consider other pathomics-focused notebooks available in the IDC-Tutorials repository: IDC-Tutorials/notebooks/pathomics at master · ImagingDataCommons/IDC-Tutorials · GitHub.