scverse / scverse/spatialdata-io
filtered_counts_file parameter for cell-segmented matrices
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visium-hd
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- Python
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Description
Hello!
Is there a chance that the filtered_counts_file parameter of the visium_hd reader can apply to cell-segmented matrices as well?
For example here, when I set the filtered_counts_file to False:
sdata = visium_hd(
path=crc_spaceranger_outs,
dataset_id='CRC',
filtered_counts_file=False,
load_segmentations_only=True
)
it still loads the number of observations in filtered_feature_cell_matrix.h5 instead of raw_feature_cell_matrix.h5.
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Research direction
Start at the visium_hd reader and trace how filtered_counts_file is handled when load_segmentations_only=True. Compare the observation count loaded from filtered_feature_cell_matrix.h5 with the expected raw_feature_cell_matrix.h5 behavior, then add or update coverage for this parameter combination.
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
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 65/100