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Add SpaceM datasets #115

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Add SpaceM datasets #115

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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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