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Published 20 hours ago • verified publisher icon scverse

Add SpaceM datasets

Open aeisenbarth opened this issue 1 year ago • 2 comments

This PR adds two SpaceM datasets to the list of example datasets.

Additionally, I suggest a notebook that visualizes and explores the contents of the dataset. Descriptions in the notebook may still be expanded a little. Also, I can remove the analysis section if it is not relevant, and just keep the visualization with spatialdata-plot.

Work still needed:

  • [x] Transfer datasets to storage
  • [x] Merge of https://github.com/giovp/spatialdata-sandbox/pull/47
  • [x] Update 4 URLs (2× .zarr.zip, 2× .zarr/) and file sizes in README.md

aeisenbarth avatar Aug 09 '24 16:08 aeisenbarth

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review-notebook-app[bot] avatar Aug 09 '24 16:08 review-notebook-app[bot]

Thanks, I updated the URLs.

Notes:

  • [x] I skipped the S3 URLs from the README because the data is still not processed and uploaded by the CI. I will do this once the problem with . in the name is addressed.
  • [x] I put the URLs for the full data in the README, and I added both the URLs for the full and small data in the notebook.
  • [x] I would not add a notebook also for the other dataset, I think one is enough.
  • [x] In the small dataset I could not plot the UMAP for "replicate", CONDITION_COL since they were not present, so I removed them.
  • [x] I added the notebook to the visualization notebooks in the docs.

Todos:

  • [x] close https://github.com/scverse/spatialdata/issues/624 before merging this PR.
  • [x] (andreas) please can you add a small icon for the docs under _static/img/spacem.png?
  • [x] (andreas) also, please add a citation file to the README, if available
  • [x] (luca) before/after merging this PR, include the notebook in the CI.

LucaMarconato avatar Aug 13 '24 15:08 LucaMarconato

@aeisenbarth going back to this, do you have a citation for the datasets? For the moment I will link the README files that you added in spatialdata-sandbox. If you think that the info contained there is enough we can keep it like this.

LucaMarconato avatar Jan 15 '25 16:01 LucaMarconato

Thanks @aeisenbarth, I reviewed the PR and closed the latest open points. Merging now!

LucaMarconato avatar Jan 20 '25 10:01 LucaMarconato

(luca) before/after merging this PR, include the notebook in the CI.

Addressed here: https://github.com/scverse/spatialdata-notebooks/pull/129

LucaMarconato avatar Jan 20 '25 13:01 LucaMarconato