No warning when the manually specified table doesn't actually annotate the labels element #467

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1. timtreis commented on May 24, 2025

   

   timtreis

   on May 24, 2025

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   Correct plot after setting it:

   
2. timtreis

   added

   enhancementNew feature or requestNew feature or request

   labels 🏷️Anything related to LabelsAnything related to Labels

   on May 24, 2025
3. VikramGanesanjs commented on Sep 9, 2025

   

   VikramGanesanjs

   on Sep 9, 2025

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   @timtreis I am having the same issue, could you explain how you are supposed to set the spatialdata_attrs to make this work? I've tried replacing the table.uns['spatialdata_attrs']['region_key'] with 'leiden', but it throws the error (Regions in the AnnData object and leiden do not match.)
4. timtreis commented on Sep 11, 2025

   

   timtreis

   on Sep 11, 2025

   Last edited by timtreis

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   Hey @VikramGanesanjs,

   here you can find an example on how to manually set it: https://github.com/scverse/spatialdata-notebooks/blob/main/notebooks/examples/sdata_from_scratch.ipynb

   the tl;dr is like this:

   table.uns["spatialdata_attrs"] = {
       "region": "<name of the sdata element it annotates>",  
       "region_key": "<column in adata.obs that will link a given obs to the elements it annotates, same entry as region>",
       "instance_key": "<column that matches a given obs in the table to a given circle by id>",
   }
   
5. timtreis

   linked a pull request that will close this issueUpdate CI/CD to use pixi and parallel testing; also moving to Python 3.11-3.13 #481on Sep 11, 2025
6. timtreis

   linked a pull request that will close this issueAdd warning if `table_name` and `color` are specified but the table doesn't annotate the element #490on Sep 23, 2025
7. timtreis

   closed this as completedin #490on Sep 23, 2025