scverse / scverse/spatialdata-io

visium_hd reader: load_segmentations_only = False still loads segmentation results

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Description

Hi, I am on spatialdata-io 0.5.1 and I noticed that for the visium_hd() reader, the load_segmentations_only=False does not strictly replicate legacy behavior.

The docstring states:

load_segmentations_only
      If `True`, only the segmented cell boundaries and their associated counts will be loaded. All binned data
      will be skipped. If `False`, only the binned data will be loaded (which is consistent with legacy behavior).
      If `None` (default), it will be equivalent to `False`, but a deprecation warning will be raised to inform users that
      in future releases the default value will be changed to `True`. To avoid the warning, explicitly set this parameter to
      `False` or `True`.

However, regardles of whether load_segmentations_only is True or False, segmentation results are loaded if present. load_segmentations_only currently only seems to have an effect on whether the binned data is loaded or not.

I think the desired behavior would indeed be that the users has a choice of whether to load the binned data, the segmentation results or both. Note that even if the reader behaved as stated in the docstring, this would then not give you the option of reading in both.

Thanks!

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Research direction

Start at the visium_hd() reader and trace how load_segmentations_only controls loading of segmentation results and binned data. Compare the implementation with the documented behavior, then define how the reader should represent loading binned data, segmentations, or both and verify each supported option.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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