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!
1 Like
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.