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ImagingDataCommons / slim

Interoperable web-based slide microscopy viewer and annotation tool
https://imagingdatacommons.github.io/slim/
Apache License 2.0
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Example multichannel image (cancer, IF) #152

Closed Elena983 closed 1 year ago

Elena983 commented 1 year ago

Hi

I would like to explore cancer images stained with different dyes (multiplex). Where can I download them?

fedorov commented 1 year ago

We have such images in Imaging Data Commons, here's one collection, HTAN-HMS: https://portal.imaging.datacommons.cancer.gov/explore/filters/?collection_id=HTAN&collection_id=htan_hms.

Here's example visualization: https://viewer.imaging.datacommons.cancer.gov/slim/studies/2.25.110940496032974123445604819863673717982/series/1.3.6.1.4.1.5962.99.1.2354479345.898820832.1655916921073.4.0?state=1.2.826.0.1.3680043.10.511.3.53242747314058586408747106697332823

If you want to download the files from that specific collection, you can follow the instructions here https://learn.canceridc.dev/data/downloading-data, and use this selection query:

SELECT gcs_url
FROM `bigquery-public-data.idc_current.dicom_all`
WHERE collection_id = "htan_hms"

Let us know if you need help with any of the above!

fedorov commented 1 year ago

Please reopen if you want to follow up and the response above was not sufficient.