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Improvement to the docs

Open LucaMarconato opened this issue 1 year ago • 6 comments

Routinely listing improvement we can make to the docs:

  • [x] add rasterize_bins() example in Visium HD notebook;
  • [ ] show how to use get_element_instances() in the annotation notebook.

LucaMarconato avatar Jul 09 '24 22:07 LucaMarconato

  • [ ] make a notebook showing how to add an existing segmentation to an object; give just an introduction and refer to SOPA tutorials for more in-depth analyses
  • [ ] put a link to the spaitaldata-xenium-explorer notebook and a link to the Squidpy Xenium notebook in the xenium spaitaldata notebook

LucaMarconato avatar Jul 11 '24 17:07 LucaMarconato

LucaMarconato avatar Sep 02 '24 09:09 LucaMarconato

Using less and simpler datasets, tracked here https://github.com/scverse/spatialdata/issues/700

LucaMarconato avatar Sep 03 '24 14:09 LucaMarconato

As suggested here from a user https://github.com/scverse/spatialdata-plot/issues/371#issuecomment-2408921406:

  • [ ] explain, in the optimization notebook of spatialdata-plot, that the data needs to be saved to disk to have the multiscale, chunked representation optimization enabled
  • [ ] make the spatialdata-plot and napari-spatialdata notebooks also available in the respective repos. Also, link them all in the spatialdata docs, in a clear section. Right now, the spatialdata-plot notebooks are stored in spatialdata-notebooks and shown in spatialdata but not in spatialdata-plot. Instead, the napari-spatialdata notebooks are stored in napari-spatialdata and shown in napari-spatialdata but not in spatialdata.

LucaMarconato avatar Oct 13 '24 10:10 LucaMarconato

  • [ ] add docs for get_element_annotators().
  • [ ] Consider moving get_annotated_regions() and get_element_annotators() to the same place, and make names more uniform.

LucaMarconato avatar Jan 21 '25 13:01 LucaMarconato

  • [ ] add get_table_keys() to the docs.

LucaMarconato avatar Apr 10 '25 21:04 LucaMarconato