From MuData to SpatialData #319
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bio-la
reviewed
Feb 11, 2025
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| ### dependencies | ||
| - pinned "spatialdata==0.2.6", "spatialdata-io==0.1.6", "dask==2024.12.1" as temporary fix |
bio-la
reviewed
Feb 11, 2025
| import os | ||
| from pathlib import Path | ||
| """ | ||
| this script copies the make_adata_from_csv.py that creates | ||
| ONE MUDATA PER SAMPLE, with in each ONE LAYER per modality |
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is this comment up to date?
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ah no! i can update it
bio-la
reviewed
Feb 12, 2025
| L.info("Reading in SpatialData from '%s'" % args.input_spatialdata) | ||
| sdata = sd.read_zarr(args.input_spatialdata) | ||
| #mdata = mu.read(args.input_spatialdata) | ||
| #spatial = mdata.mod['spatial'] |
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is it expected that at this checkpoint you don't offer the option to read a mudata anymore?
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expected from what? the plot_qc_spatial.py file gets .zarr files as input from the pipeline in qc and preprocessing
bio-la
reviewed
Feb 12, 2025
| L.info("Reading in spatial MuData from '%s'" % args.input_spatial) | ||
| mdata_spatial = mu.read(args.input_spatial) | ||
| adata_st = mdata_spatial.mod['spatial'] | ||
| L.info("Reading in spatial SpatialData from '%s'" % args.input_spatial) |
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cell2location only accepts spatialData now
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yes. do you want cell2location to also run on MuData/AnnData?
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Hi!
I adjusted both the Ingestion and the Preprocessing to SpatialData. I also added the ingestion for xenium
I can, as a next step, adjust the github actions and tutorials.