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Use scanpy for reading matrixes #288

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LucaMarconato opened this issue Mar 15, 2025 · 0 comments
Open

Use scanpy for reading matrixes #288

LucaMarconato opened this issue Mar 15, 2025 · 0 comments

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@LucaMarconato
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We currently have a the custom implementation for reading matrices (copied from scanpy) in https://github.com/scverse/spatialdata-io/blob/main/src/spatialdata_io/readers/_utils/_read_10x_h5.py.

I would remove that code and use directly scanpy, which is already a dependency. I think initially the code was copied to minimize the number of dependencies (@giovp what this the case?) but then we chose to add scanpy anyway.

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