spatialdata
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Improvement to the docs
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.
- [ ] 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
- [x] add an example of
transform()in the transformations notebook (suggested by "liz-is" via Discourse)
Using less and simpler datasets, tracked here https://github.com/scverse/spatialdata/issues/700
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-plotandnapari-spatialdatanotebooks also available in the respective repos. Also, link them all in thespatialdatadocs, in a clear section. Right now, thespatialdata-plotnotebooks are stored inspatialdata-notebooksand shown inspatialdatabut not inspatialdata-plot. Instead, thenapari-spatialdatanotebooks are stored innapari-spatialdataand shown innapari-spatialdatabut not inspatialdata.
- [ ] add docs for
get_element_annotators(). - [ ] Consider moving
get_annotated_regions()andget_element_annotators()to the same place, and make names more uniform.
- [ ] add
get_table_keys()to the docs.