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Add SpaceM datasets #115

Merged
merged 9 commits into from
Jan 20, 2025
Merged

Add SpaceM datasets #115

merged 9 commits into from
Jan 20, 2025

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aeisenbarth
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@aeisenbarth aeisenbarth commented Aug 9, 2024

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:

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@LucaMarconato
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LucaMarconato commented Aug 13, 2024

Thanks, I updated the URLs.

Notes:

  • 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.
  • 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.
  • I would not add a notebook also for the other dataset, I think one is enough.
  • In the small dataset I could not plot the UMAP for "replicate", CONDITION_COL since they were not present, so I removed them.
  • I added the notebook to the visualization notebooks in the docs.

Todos:

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LucaMarconato commented Jan 15, 2025

@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 LucaMarconato marked this pull request as ready for review January 20, 2025 10:29
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Thanks @aeisenbarth, I reviewed the PR and closed the latest open points. Merging now!

@LucaMarconato LucaMarconato merged commit 0a2a1c1 into scverse:main Jan 20, 2025
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@LucaMarconato
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(luca) before/after merging this PR, include the notebook in the CI.

Addressed here: #129

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